From gwaldon at geneinfinity.org  Fri Apr  1 20:11:02 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Fri, 01 Apr 2011 19:11:02 -0500
Subject: [Biojava-l] Expasy pI calculation algorythm
Message-ID: <20110401191102.44902rooroy3x9k4@gator1273.hostgator.com>

Hello,

Sorry if this comes a bit late; we had to solve some email issues -  
Thanks again to Andreas for doing it.

This is part of the email exchange I had with Christine Hoogland and  
Gregoire Rossier a few years ago regarding the algorithm used by  
"Compute pI/Mw" on the Expazy server. The code which was given to me  
is included at the end of this email; I used it to update bj1.

Good luck to all GSoC candidates,

George


On Tue, May 22, 2007 at 9:26 AM, Christine Hoogland via RT  
<tools at expasy.org> wrote:

     Dear George,

     Please find enclosed the algorithm we are using on ExPASy.

     I hope this helps.

     Best regards
     Christine

     >
     > The pK values used for "Compute pI/Mw" can be found in
     >
     > # Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
     > Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing
     > positions of polypeptides in immobilized pH gradients can be predicted
     > from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
     >
     > MEDLINE: 8125050
     >
     > # Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference
     > points
     > for comparisons of two-dimensional maps of proteins from different
     > human
     > cell types defined in a pH scale where isoelectric points correlate
     > with
     > polypeptide compositions. Electrophoresis 1994, 15, 529-539.
     >
     > MEDLINE: 8055880
     >
     > The pK were defined by examining polypeptide migration between pH 4.5
     > to
     > 7.3 in an immobilised pH gradient gel environment with 9.2M and 9.8M
     > urea at 15?C or 25?C. Prediction of protein pI for highly basic
     > proteins
     > is yet to be studied and it is possible that current Compute pI/Mw
     > predictions may not be adequate for this purpose.
     >
     > I hope this helps.
     >
     >
     > Best regards
     > Gregoire Rossier
     >
     >

     --------------------------------------------------------
     Christine Hoogland
     Swiss Institute of Bioinformatics
     CMU - 1, rue Michel Servet      Tel. (+41 22) 379 58 28
     CH - 1211 Geneva 4 Switzerland  Fax  (+41 22) 379 58 58
     Christine.Hoogland at isb-sib.ch   http://www.expasy.org/
     --------------------------------------------------------

     //  VERSION      :   1.6
     //  DATE         :   1/25/95
     //  Copyright 1993 by Swiss Institute of Bioinformatics. All  
rights reserved.

     //
     // Table of pk values :
     //  Note: the current algorithm does not use the last two columns. Each
     //  row corresponds to an amino acid starting with Ala. J, O and U are
     //  inexistant, but here only in order to have the complete alphabet.
     //
     //     Ct    Nt   Sm     Sc     Sn
     //

     static double cPk[26][5] = {
     3.55, 7.59, 0.   , 0.   , 0.    , // A
     3.55, 7.50, 0.   , 0.   , 0.    , // B
     3.55, 7.50, 9.00 , 9.00 , 9.00  , // C
     4.55, 7.50, 4.05 , 4.05 , 4.05  , // D
     4.75, 7.70, 4.45 , 4.45 , 4.45  , // E
     3.55, 7.50, 0.   , 0.   , 0.    , // F
     3.55, 7.50, 0.   , 0.   , 0.    , // G
     3.55, 7.50, 5.98 , 5.98 , 5.98  , // H
     3.55, 7.50, 0.   , 0.   , 0.    , // I
     0.00, 0.00, 0.   , 0.   , 0.    , // J
     3.55, 7.50, 10.00, 10.00, 10.00 , // K
     3.55, 7.50, 0.   , 0.   , 0.    , // L
     3.55, 7.00, 0.   , 0.   , 0.    , // M
     3.55, 7.50, 0.   , 0.   , 0.    , // N
     0.00, 0.00, 0.   , 0.   , 0.    , // O
     3.55, 8.36, 0.   , 0.   , 0.    , // P
     3.55, 7.50, 0.   , 0.   , 0.    , // Q
     3.55, 7.50, 12.0 , 12.0 , 12.0  , // R
     3.55, 6.93, 0.   , 0.   , 0.    , // S
     3.55, 6.82, 0.   , 0.   , 0.    , // T
     0.00, 0.00, 0.   , 0.   , 0.    , // U
     3.55, 7.44, 0.   , 0.   , 0.    , // V
     3.55, 7.50, 0.   , 0.   , 0.    , // W
     3.55, 7.50, 0.   , 0.   , 0.    , // X
     3.55, 7.50, 10.00, 10.00, 10.00 , // Y
     3.55, 7.50, 0.   , 0.   , 0.    }; // Z

     #define PH_MIN 0 /* minimum pH value */
     #define PH_MAX 14 /* maximum pH value */
     #define MAXLOOP 2000 /* maximum number of iterations */
     #define EPSI 0.0001 /* desired precision */

       //
       // Compute the amino-acid composition.
       //
       for (i = 0; i < sequenceLength; i++)
         comp[sequence[i] - 'A']++;

       //
       // Look up N-terminal and C-terminal residue.
       //
       nTermResidue = sequence[0] - 'A';
       cTermResidue = sequence[sequenceLength - 1] - 'A';

       phMin = PH_MIN;
       phMax = PH_MAX;

       for (i = 0, charge = 1.0; i < MAXLOOP && (phMax - phMin) > EPSI; i++)
         {
           phMid = phMin + (phMax - phMin) / 2;

           cter = exp10(-cPk[cTermResidue][0]) /
      (exp10(-cPk[cTermResidue][0]) + exp10(-phMid));
           nter = exp10(-phMid) /
      (exp10(-cPk[nTermResidue][1]) + exp10(-phMid));

           carg = comp[R] * exp10(-phMid) /
      (exp10(-cPk[R][2]) + exp10(-phMid));
           chis = comp[H] * exp10(-phMid) /
      (exp10(-cPk[H][2]) + exp10(-phMid));
           clys = comp[K] * exp10(-phMid) /
      (exp10(-cPk[K][2]) + exp10(-phMid));

           casp = comp[D] * exp10(-cPk[D][2]) /
      (exp10(-cPk[D][2]) + exp10(-phMid));
           cglu = comp[E] * exp10(-cPk[E][2]) /
      (exp10(-cPk[E][2]) + exp10(-phMid));

           ccys = comp[C] * exp10(-cPk[C][2]) /
      (exp10(-cPk[C][2]) + exp10(-phMid));
           ctyr = comp[Y] * exp10(-cPk[Y][2]) /
      (exp10(-cPk[Y][2]) + exp10(-phMid));

           charge = carg + clys + chis + nter -
      (casp + cglu + ctyr + ccys + cter);

           if (charge > 0.0)
              phMin = phMid;
           else
              phMax = phMid;
         }
       }



From frieman6 at gmail.com  Mon Apr  4 08:59:50 2011
From: frieman6 at gmail.com (omer f)
Date: Mon, 4 Apr 2011 15:59:50 +0300
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
Message-ID: <BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>

To all it may concern,

Dear BioJava,

My name Omer Frieman and i am a student of Computer Science (B.Sc) and
International Politics at the Hebrew university in Jerusalem, Israel.
Last week, I attended a conference about Google SOC, Which i find most
interesting and something that i would like to experience.
I am in the second year of my degree, and so far i have learned the program
languages: Java, C, C++ and in addition Object Oriented Programming in Java.
Though, i have no working experience in programming.

While searching the list of SOC projects i came across the Bioinformatics
Foundation Projects.
I found the Java Project very interesting, First, for the content - the
research subject of Bio-informatics, and Second, I was looking specifically
for a Java project for gaining experience in it,

Before sending my application with the short coding exercise, i send you
this mail to Introduce myself.
My only concern is,  will My lack of experience could hurt my chances to be
accepted to the project.
I would appreciate  your opinion in that matter.

Furthermore, i was wondering how do i connect the Project mentor (Peter
Troshin).

Sincerely,
 Omer.

From p.v.troshin at dundee.ac.uk  Mon Apr  4 10:33:38 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Mon, 04 Apr 2011 15:33:38 +0100
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
	<BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>
Message-ID: <4D99D6C2.9060107@dundee.ac.uk>

Hi Omer,

I am on the BioJava list so I got your email.

> >> I am in the second year of my degree, and so far i have learned
> >> the program languages: Java, C, C++ and in addition Object
> >> Oriented Programming in Java.

Sounds good!

> >> Though, i have no working experience in programming.

Thank you for being honest (:-))

> >> My only concern is, will My lack of experience could hurt my
> >> chances to be accepted to the project.

It may but it may not. Some people pick up things pretty quickly - are 
you one of them?
Seriously, have a look at the methods that you are about to implement, 
search the web
for more information about them and see if you have a good idea how to 
do that. You do not have to know anything about the BioJava at this 
stage, you can learn about it later.  For this
project you also need to know the basics of Chemistry and Molecular 
Biology, nothing too
complicated, but still without this knowledge the learning curve for 
this project is going to be pretty steep.

I hope I answered your question.

Regards,
Peter



On 04/04/2011 13:59, omer f wrote:
>  To all it may concern,
>
>  Dear BioJava,
>
>  My name Omer Frieman and i am a student of Computer Science (B.Sc)
>  and International Politics at the Hebrew university in Jerusalem,
>  Israel. Last week, I attended a conference about Google SOC, Which i
>  find most interesting and something that i would like to experience.
>  I am in the second year of my degree, and so far i have learned the
>  program languages: Java, C, C++ and in addition Object Oriented
>  Programming in Java. Though, i have no working experience in
>  programming.
>
>  While searching the list of SOC projects i came across the
>  Bioinformatics Foundation Projects. I found the Java Project very
>  interesting, First, for the content - the research subject of
>  Bio-informatics, and Second, I was looking specifically for a Java
>  project for gaining experience in it,
>
>  Before sending my application with the short coding exercise, i send
>  you this mail to Introduce myself. My only concern is, will My lack
>  of experience could hurt my chances to be accepted to the project. I
>  would appreciate your opinion in that matter.
>
>  Furthermore, i was wondering how do i connect the Project mentor
>  (Peter Troshin).
>
>  Sincerely, Omer. _______________________________________________
>  Biojava-l mailing list - Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l



From x4roth at gmail.com  Mon Apr  4 11:34:13 2011
From: x4roth at gmail.com (Xaroth)
Date: Mon, 4 Apr 2011 11:34:13 -0400
Subject: [Biojava-l] GSoC Intent - Amino Acids Physico-Chemical Properties
	Calculation
Message-ID: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>

Hello everyone and project mentor Peter Troshin,

My name is Justin Pugh. I am a 3rd year Computer Science student at the
University of Central Florida. I am proficient in C and Java and I prefer to
do all of my coding work in Java. I've recently learned about the Google
Summer of Code program and I've been spending the past week or so looking
over the available open-source projects. I am excited about participating in
the GSoC because I have been anxious to be a part of a larger project than
the small-scope programs that I have to write for classes. Sadly, I do not
have any experience doing any programming projects on this scale but I am
very interested in learning. The largest project I have completed was to
write a compiler and virtual machine for PL/0. I'm currently working on
writing a game from scratch as a vehicle for implementing some AI techniques
and I am learning a lot about making use of others' code provided in
libraries and integrating it into my own through the use of jMonkeyEngine
(an open source java-based 3d game engine). I want to take my skills to the
next level with GSoC.

Out of all the projects I have looked at, BioJava has stood out the most for
me (in particular, the Amino Acids Physico-Chemical Properties Calculation
idea). I wanted to work on something written entirely in Java so I wouldnt
have to spend any time learning a new language and I would be able to focus
more on the actual project. I feel like I am able to wrap my head around the
Amino Acids Physico-Chemical Properties Calculation proposal and I think it
falls within my ability to get it done and even more - to have fun with it
and be able to spend time refining it. I do not know anything about the
calculations which must be implemented, but I am of course willing to learn
them. I have only had small instruction in the area of multi-threaded Java
programming but I hope this will not be a severe handicap for me.

I plan on spending the next couple days doing some research and developing
my proposal. I just wanted to announce my intent to submit an application
and to introduce myself to the group. Please let me know your opinions
regarding my ability to complete this project - I am open to criticism and
pointers! :)

Thank you for your time,
-Justin Pugh

From p.v.troshin at dundee.ac.uk  Tue Apr  5 06:23:10 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 11:23:10 +0100
Subject: [Biojava-l] GSoC Intent - Amino Acids Physico-Chemical
 Properties Calculation
In-Reply-To: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
References: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
Message-ID: <4D9AED8E.3070309@dundee.ac.uk>

Hi Justin,

Welcome to the BioJava mailing list and thank you for your interest in 
the project.

It sounds like you have plenty of experience in programming, which is 
definitely a plus. Do not worry about you lack of experience in 
multi-threaded programs, in the end there must be something for you to 
learn too! I hope that this project can give you what you are looking 
for ? the experience of implementing algorithms in pure Java and 
integrating with the relatively large BioJava code base.

However, do not underestimate the difficulty of the algorithms for 
calculating the physico-chemical properties. Although the algorithms may 
not be particularly complex, but in order to understand them you would 
need some knowledge in chemistry, molecular biology and maths. 
Programming skills only will not be sufficient for this project.

Good luck with your application.

Regards,
Peter





On 04/04/2011 16:34, Xaroth wrote:
> Hello everyone and project mentor Peter Troshin,
>
> My name is Justin Pugh. I am a 3rd year Computer Science student at the
> University of Central Florida. I am proficient in C and Java and I prefer to
> do all of my coding work in Java. I've recently learned about the Google
> Summer of Code program and I've been spending the past week or so looking
> over the available open-source projects. I am excited about participating in
> the GSoC because I have been anxious to be a part of a larger project than
> the small-scope programs that I have to write for classes. Sadly, I do not
> have any experience doing any programming projects on this scale but I am
> very interested in learning. The largest project I have completed was to
> write a compiler and virtual machine for PL/0. I'm currently working on
> writing a game from scratch as a vehicle for implementing some AI techniques
> and I am learning a lot about making use of others' code provided in
> libraries and integrating it into my own through the use of jMonkeyEngine
> (an open source java-based 3d game engine). I want to take my skills to the
> next level with GSoC.
>
> Out of all the projects I have looked at, BioJava has stood out the most for
> me (in particular, the Amino Acids Physico-Chemical Properties Calculation
> idea). I wanted to work on something written entirely in Java so I wouldnt
> have to spend any time learning a new language and I would be able to focus
> more on the actual project. I feel like I am able to wrap my head around the
> Amino Acids Physico-Chemical Properties Calculation proposal and I think it
> falls within my ability to get it done and even more - to have fun with it
> and be able to spend time refining it. I do not know anything about the
> calculations which must be implemented, but I am of course willing to learn
> them. I have only had small instruction in the area of multi-threaded Java
> programming but I hope this will not be a severe handicap for me.
>
> I plan on spending the next couple days doing some research and developing
> my proposal. I just wanted to announce my intent to submit an application
> and to introduce myself to the group. Please let me know your opinions
> regarding my ability to complete this project - I am open to criticism and
> pointers! :)
>
> Thank you for your time,
> -Justin Pugh
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From p.v.troshin at dundee.ac.uk  Tue Apr  5 12:00:32 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 17:00:32 +0100
Subject: [Biojava-l] Final Application (Paiu Alexandru ) (added project
 plan)
In-Reply-To: <AANLkTin9Ggi1KMERJ157sxzFbXu9=qFrJi+WRdq0JH=j@mail.gmail.com>
References: <AANLkTin9Ggi1KMERJ157sxzFbXu9=qFrJi+WRdq0JH=j@mail.gmail.com>
Message-ID: <4D9B3CA0.6000707@dundee.ac.uk>

Hi Alex,

I have a look at your plan and I'd suggest that you add a few more 
details into it. Right now I'd say it does not look sufficiently detailed.

What are the deliverables of you project?
What steps you will take at every stage of the project.
How you make sure that your implementation gives the correct results?
Are you going to use BioJava? If so how?

Also, I would not bother with any implementation details as yet.
Finally, If you worked with any version control systems it would help to 
state this.

I hope this will help you to improve your proposal.

Regards,
Peter


On 28/03/2011 17:17, Alexandru Paiu wrote:
> *1.      **1.Your complete contact information*, including full name,
> physical address, preferred email address, and telephone number, plus other
> pertinent contact information such as IRC handles, etc.
>
>
>
> Full Name : Paiu Alexandru
>
> Address : Country Romania , city Constanta , Bld. Aurel Vlaicu , Nr. 41 ,
> Bl. Pc1 sc. B , Et 6 , Apt. 46
>
> E-mail : paiualex12 at google.com or paiualex12 at yahoo.com
>
> Telephone number : 40733924684
>
>
>
> *2.       **2.Why you are interested in the p*roject you are proposing and
> are well-suited to undertake it.
>
>
>
> This project suits me perfectly , because the interested students should
> have a general knowledge of core Java programming, knowledge of
> multi-threaded programming . I?ve started learning Java for 1 and a half
> years , and I used a lot of Threads in applications and projects .
>
> This is the only project that I apply , because I haven?t found a more
> interesting project than this one .
>
>
>
> *3.       **3.A summary of your programming *experience and skills.
>
>
>
> I?ve did a lot of miniproject and applications for school and for me . I?ve
> made projects like :
>
> a)      Lanchat Client-Server using TCP/IP ? I wrote two applications : one
> for the client and one for the server . I used an JApplet for the client
> with Swing elements . I?ve used Threads especially in the server sider
> application , and sockets
>
> b)      Lanchat Peer-to-Peer using UDP and multicasting . I wrote only a
> application for  the client . I used Threads and multicast sockets .
>
> c)       A project for administrating a database , using a JApplet with
> Connector/J and MySql . It has to applications , one for clients and for the
> administrator .
>
>
> *4.        **4.Programs or projects you have previously* authored or
> contributed to  available as open-source, including, if applicable, any past
> Summer of Code involvement.
>
>
>
> I haven?t worked yet for any open-source and a I haven?t any past experience
> with GSoc , and it?s the first time a apply for a open-source project . I
> haven?t either worked for a company .
>
>
>
> *5.       **5. A project plan for the project* you are proposing, even if
> your proposed project is directly based on one of the proposed project ideas
> for member projects.
>
>
>
> I wish to apply to the project called *Amino Acids physic-chemical
> properties calculation .*
>
> I?ve been thinking since some time of a possible implementation and I
> stopped at a single one (that I think it?s the best) .
>
>
>
> I will use two main classes . One that will represent an atom of a substance
> ( for example He , H , O , etc ) , that will have params like : atom weight
> , name , abbreviation , valence .  I?ll use the second class for
> constructing amino-acids from this class . So , the second class will extend
> the class of atoms . So for example I have to initiate a molecule of H20
> (water) . I will have a constructor with a string param , that will build
> the substance . For example , let?s say that the second class it?s called
> Aminoacids , and the first one Atoms .
>
> Let?s say I choose from a Combo box H2O ( it?s only a example) . Then I sad
> the string ? H2O1? to the aminoacids class , to intiate an object of
> aminoacid . That constructor will be evaluated char by char . If it?s found
> a char or two chars that means that I have to initiate an atom of that char
> or chars . If it?s found a number , then that means that it?s the multiplier
> of that atom before it .
>
> So the class aminoacids will have a private Object [] array , in which will
> be number and objects called atoms .
>
> So for H20 the array will look like this : array[0] = atom of H (Hidrogen) ,
> array[1]=2 , array[2]=O (Oxigen) , array[3]=1 .
>
> All the know substances will be in a file called atoms.txt with atom mass ,
> name , abbreviation etc . The atoms class will have a method to add new
> atoms to the list .
>
>
>
> And for calculating the molecular weigth the algorithm is very simple . We
> already have array={H,2,O,1} , and the atoms will have as params the atoms
> weight so all we have to do is just :
>
> Mol. Weight=H.weight*2+O.weigth.*1
>
>
>
> The plan for implementing :
>
>
>
> -          May 20-June 20 ? implementing the two classes and the first two
> methods
>
> -          June 20 ? 20 July ? Implementing the rest of the methods
>
> -          20 July ? until the final ? final retouching , docummentation for
> end users , and 1  method proposed by me
>
> -
>
> *6.       **6.Any obligations, vacations, or plans* for the summer that may
> require scheduling during the GSoC work period.
>
>
>
> I will have School final exams during 20 May ? 20 June . So I won?t be able
> to work at maximum capacity . That?s all . I
>
>
> *7. PS *
>
> I hope you've got my short coding exercise program ( I received a kinda
> error for sending a mail will atachement)
>
> thanks
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l


From p.v.troshin at dundee.ac.uk  Tue Apr  5 12:44:08 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 17:44:08 +0100
Subject: [Biojava-l] attention to GSoC Amino Acids Physico-Chemical
 Properties prospective students
In-Reply-To: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
References: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
Message-ID: <4D9B46D8.6070906@dundee.ac.uk>

Hello prospective GSoC students,

A have seen a few project plans so far and none of them seems to go into 
the trouble of providing the formulas for the calculations. Yet, it 
would have definitely strengthened your proposal if you can demonstrate 
that you are capable of extracting this information from the web and/or 
scientific papers. That said you do not have to include everything in 
your proposal but at least show that you know where to find what you 
need. There is the balance here to strike and this is something that is 
going to set you apart.

I'd like to stress that the ideal student for this project should not 
only be a good Java programmer but have a keen interest in 
Bioinformatics! So please feel free to extend the original idea as you 
see fit.

Good luck with your applications,
Peter

P.S.
The project plan is if of cause yours and you should decide whether to 
include anything from the above or leave it, this is only an advice.

Dr Peter Troshin
Bioinformatics Software Developer
Phone: +44 (0)1382 388589
Fax:     +44 (0)1382 385764
The Barton Group
College of Life Sciences
Medical Sciences Institute
University of Dundee
Dundee
DD1 5EH
UK


From andreas at sdsc.edu  Wed Apr  6 00:33:47 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 5 Apr 2011 21:33:47 -0700
Subject: [Biojava-l] last days before submitting for GSoC
Message-ID: <BANLkTim95ye4eNChNyoDdUYbSFcRhOOkPQ@mail.gmail.com>

Hi,

just a quick reminder that the deadline to submit proposals for GSoC
is approaching rapidly (Friday).

In order to correctly apply you need to submit your applications at

http://www.google-melange.com/

Don't forget to discuss your projects with the potential mentors or this list.

A couple of more links that might be useful:

how to write a proposal
http://www.booki.cc/gsocstudentguide/_v/1.0/writing-a-proposal/

Here two proposals that got funded last year:

http://biojava.org/wiki/GSoC:MSA
http://biojava.org/wiki/GSoC:PTM

Andreas

From madhatterkkt at gmail.com  Wed Apr  6 00:37:47 2011
From: madhatterkkt at gmail.com (K T)
Date: Tue, 5 Apr 2011 21:37:47 -0700
Subject: [Biojava-l] Retrieving data from Genbank online
Message-ID: <BANLkTi=qC4-kkqjvYTf4BZanTZLUuTnkUg@mail.gmail.com>

I'm new to BioJava3, and recently downloaded 3.0.1.  I'm looking for a way
to retrieve entries from NCBI online (not a flat-file) using a RefSeq
accession ID.  I was able to do this with BioPerl, and I've also seen that
there was a way to do this under BioJava 1.x.  Can someone point me to a
code-snippet where this is done for BioJava3?

I tried searching online, but most of my search hits point either to BioJava
1.x or refer to retrieving them from a flat-file.  I'm trying to get it from
NCBI's online database directly.

Thanks in advance.

From alastair.m.kilpatrick at googlemail.com  Wed Apr  6 05:07:27 2011
From: alastair.m.kilpatrick at googlemail.com (Alastair Kilpatrick)
Date: Wed, 6 Apr 2011 10:07:27 +0100
Subject: [Biojava-l] Multiple sequence alignment in BioJava
Message-ID: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>

Dear all,
I'm pretty new to BioJava so I may be missing something - I've checked
through the list archives without much luck.
I've been trying to do some multiple sequence alignments but I've been
running into strange errors. To try and find where the problem is,
I've just copied the code straight from
http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
I'm still getting an error:

Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix

It would seem that this is something to do with forester.jar, which I
had to download separately (from http://code.google.com/p/forester/)
as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
when I look through the jar in Eclipse, there isn't anything named
'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
'phylogeny.factories' and 'phylogeny.iterators'. Is there something
I'm doing wrong, or is it the case that either one of BioJava or
forester has been updated and things have broken somewhere (I see the
CookBook page was updated in July 2010 but forester was updated just
last month)? Either way, any ideas would be much appreciated!

Many thanks,
Alastair Kilpatrick

PhD candidate,
School of Informatics, University of Edinburgh

From alastair.m.kilpatrick at googlemail.com  Wed Apr  6 12:40:26 2011
From: alastair.m.kilpatrick at googlemail.com (Alastair Kilpatrick)
Date: Wed, 6 Apr 2011 17:40:26 +0100
Subject: [Biojava-l] Multiple sequence alignment in BioJava
In-Reply-To: <BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
References: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>
	<BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
Message-ID: <BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>

Thanks - I had just downloaded the BioJava jars manually so that's
fixed the CookBook code. However, I've made some changes in order to
align DNA sequences instead and am running into more errors - this
code:

	public static void main(String[] args) {
		String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"};
		List<DNASequence> lst = new ArrayList<DNASequence>();
		for(String seq : seqs) {
			lst.add(new DNASequence(seq));
		}
		Profile<DNASequence, NucleotideCompound> profile =
Alignments.getMultipleSequenceAlignment(lst); //**
		System.out.println(profile);
		ConcurrencyTools.shutdown();
	}

gives:
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
	at java.util.concurrent.FutureTask.get(Unknown Source)
	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
	at CookbookMSA.main(CookbookMSA.java:49)

at the 'alignment' line (**) - not sure what the problem is here, I
see that getMultipleSequenceAlignment() has an extra argument(s) in
the Javadoc but these weren't required in the example?
Final question (hopefully!) - once I have the alignments I require I'd
like to create a sequence logo - is there a way of doing this in
BioJava3? From a google search I've seen references to
DistributionTools.distOverAlignment() and similar, but can't find
anything like that in the new api.

Thanks again, sorry everyone for all the questions!

Alastair


On 6 April 2011 12:09, Scooter Willis <willishf at gmail.com> wrote:
>
> You need to use the forester.jar file from the biojava3 code check out. If you are using maven this should be automatic.
>
> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" <alastair.m.kilpatrick at googlemail.com> wrote:
>
> Dear all,
> I'm pretty new to BioJava so I may be missing something - I've checked
> through the list archives without much luck.
> I've been trying to do some multiple sequence alignments but I've been
> running into strange errors. To try and find where the problem is,
> I've just copied the code straight from
> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
> I'm still getting an error:
>
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
>
> It would seem that this is something to do with forester.jar, which I
> had to download separately (from http://code.google.com/p/forester/)
> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
> when I look through the jar in Eclipse, there isn't anything named
> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something
> I'm doing wrong, or is it the case that either one of BioJava or
> forester has been updated and things have broken somewhere (I see the
> CookBook page was updated in July 2010 but forester was updated just
> last month)? Either way, any ideas would be much appreciated!
>
> Many thanks,
> Alastair Kilpatrick
>
> PhD candidate,
> School of Informatics, University of Edinburgh
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From paiualex12 at gmail.com  Wed Apr  6 13:05:38 2011
From: paiualex12 at gmail.com (Alexandru Paiu)
Date: Wed, 6 Apr 2011 20:05:38 +0300
Subject: [Biojava-l] Identified bug in BioJava(Paiu Alexandru)
Message-ID: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>

Hi to all .
I've identified a bug in BioJava .
Usually the first element in an array is on index 0 (pos 0 ) .
I've tried to learn more about Java and I've tryed the next 2 instructions :

ProteinSequence a=new ProteinSequence("A");
AminoAcidCompound b=a.getCompoundAt(0);


This will give a null execption (out of array bounds or something like that
) .
when I put AminoAcidCompound b=a.getCompoundAt(1);  it works and identifies
the first
aminoacid as Alanine .

That's all for today

From willishf at ufl.edu  Wed Apr  6 14:30:11 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Wed, 6 Apr 2011 14:30:11 -0400
Subject: [Biojava-l] Identified bug in BioJava(Paiu Alexandru)
In-Reply-To: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>
References: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>
Message-ID: <BANLkTi=hf1ygb0_xq=_rzcFjY+QAMbJyTw@mail.gmail.com>

Alexandru

To make it easier on how biologist think about the first position(1)
versus how computer scientists think(0) we opted to go with the
biologist view of the world. So use 1 for the first sequence position.

Thanks

Scooter

On Wed, Apr 6, 2011 at 1:05 PM, Alexandru Paiu <paiualex12 at gmail.com> wrote:
> Hi to all .
> I've identified a bug in BioJava .
> Usually the first element in an array is on index 0 (pos 0 ) .
> I've tried to learn more about Java and I've tryed the next 2 instructions :
>
> ProteinSequence a=new ProteinSequence("A");
> AminoAcidCompound b=a.getCompoundAt(0);
>
>
> This will give a null execption (out of array bounds or something like that
> ) .
> when I put AminoAcidCompound b=a.getCompoundAt(1); ?it works and identifies
> the first
> aminoacid as Alanine .
>
> That's all for today
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From andreas at sdsc.edu  Thu Apr  7 01:03:40 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 6 Apr 2011 22:03:40 -0700
Subject: [Biojava-l] Multiple sequence alignment in BioJava
In-Reply-To: <BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>
References: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>
	<BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
	<BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>
Message-ID: <BANLkTi==xE9cSfejyuDO_84WmrtdE6JHDA@mail.gmail.com>

Hi Alastair,

BioJava 1.X can do distributions, however there is no counterpart for
this yet in BioJava 3.

Andreas

On Wed, Apr 6, 2011 at 9:40 AM, Alastair Kilpatrick
<alastair.m.kilpatrick at googlemail.com> wrote:
> Thanks - I had just downloaded the BioJava jars manually so that's
> fixed the CookBook code. However, I've made some changes in order to
> align DNA sequences instead and am running into more errors - this
> code:
>
> ? ? ? ?public static void main(String[] args) {
> ? ? ? ? ? ? ? ?String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"};
> ? ? ? ? ? ? ? ?List<DNASequence> lst = new ArrayList<DNASequence>();
> ? ? ? ? ? ? ? ?for(String seq : seqs) {
> ? ? ? ? ? ? ? ? ? ? ? ?lst.add(new DNASequence(seq));
> ? ? ? ? ? ? ? ?}
> ? ? ? ? ? ? ? ?Profile<DNASequence, NucleotideCompound> profile =
> Alignments.getMultipleSequenceAlignment(lst); //**
> ? ? ? ? ? ? ? ?System.out.println(profile);
> ? ? ? ? ? ? ? ?ConcurrencyTools.shutdown();
> ? ? ? ?}
>
> gives:
> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> ? ? ? ?at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
> ? ? ? ?at java.util.concurrent.FutureTask.get(Unknown Source)
> ? ? ? ?at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> ? ? ? ?at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> ? ? ? ?at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
> ? ? ? ?at CookbookMSA.main(CookbookMSA.java:49)
>
> at the 'alignment' line (**) - not sure what the problem is here, I
> see that getMultipleSequenceAlignment() has an extra argument(s) in
> the Javadoc but these weren't required in the example?
> Final question (hopefully!) - once I have the alignments I require I'd
> like to create a sequence logo - is there a way of doing this in
> BioJava3? From a google search I've seen references to
> DistributionTools.distOverAlignment() and similar, but can't find
> anything like that in the new api.
>
> Thanks again, sorry everyone for all the questions!
>
> Alastair
>
>
> On 6 April 2011 12:09, Scooter Willis <willishf at gmail.com> wrote:
>>
>> You need to use the forester.jar file from the biojava3 code check out. If you are using maven this should be automatic.
>>
>> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" <alastair.m.kilpatrick at googlemail.com> wrote:
>>
>> Dear all,
>> I'm pretty new to BioJava so I may be missing something - I've checked
>> through the list archives without much luck.
>> I've been trying to do some multiple sequence alignments but I've been
>> running into strange errors. To try and find where the problem is,
>> I've just copied the code straight from
>> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
>> I'm still getting an error:
>>
>> Caused by: java.lang.ClassNotFoundException:
>> org.forester.phylogenyinference.DistanceMatrix
>>
>> It would seem that this is something to do with forester.jar, which I
>> had to download separately (from http://code.google.com/p/forester/)
>> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
>> when I look through the jar in Eclipse, there isn't anything named
>> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
>> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something
>> I'm doing wrong, or is it the case that either one of BioJava or
>> forester has been updated and things have broken somewhere (I see the
>> CookBook page was updated in July 2010 but forester was updated just
>> last month)? Either way, any ideas would be much appreciated!
>>
>> Many thanks,
>> Alastair Kilpatrick
>>
>> PhD candidate,
>> School of Informatics, University of Edinburgh
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From effat34 at gmail.com  Thu Apr  7 07:26:43 2011
From: effat34 at gmail.com (effat farhana)
Date: Thu, 7 Apr 2011 17:26:43 +0600
Subject: [Biojava-l] Amino acids physico-chemical properties calculation
Message-ID: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>

Hi,
I'm a student of Computer Science and Engineering background. I heard about
GSoC a few days earlier and very much eager to participate in it. I'm quite
familiar with C++, Java multithreading. The idea of this project proposal
seems quite interesting to me.

One of the methods to be implemented is to calculate the numbers of
different amino  acids in protein.
Would you please explain how the input of this method will be given? Will
the protein sequence be represented by String as sequence of amino acids and
I've just count the different types of amino acid?


Looking forward for your quick reply
Thanks in advance

farhana

From p.v.troshin at dundee.ac.uk  Thu Apr  7 17:47:20 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 07 Apr 2011 22:47:20 +0100
Subject: [Biojava-l] Amino acids physico-chemical properties calculation
In-Reply-To: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>
References: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>
Message-ID: <4D9E30E8.3090501@dundee.ac.uk>

> >> Would you please explain how the input of this method will be
> >> given?

Just assume that this would be a String for now. For example 
"MFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR".

Hope that helps.

Regards,
Peter

On 07/04/2011 12:26, effat farhana wrote:
>  Hi, I'm a student of Computer Science and Engineering background. I
>  heard about GSoC a few days earlier and very much eager to
>  participate in it. I'm quite familiar with C++, Java multithreading.
>  The idea of this project proposal seems quite interesting to me.
>
>  One of the methods to be implemented is to calculate the numbers of
>  different amino acids in protein. Would you please explain how the
>  input of this method will be given? Will the protein sequence be
>  represented by String as sequence of amino acids and I've just count
>  the different types of amino acid?
>
>
>  Looking forward for your quick reply Thanks in advance
>
>  farhana _______________________________________________ Biojava-l
>  mailing list - Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l



From p.v.troshin at dundee.ac.uk  Thu Apr  7 18:26:39 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 07 Apr 2011 23:26:39 +0100
Subject: [Biojava-l] google summer of code proposal
In-Reply-To: <BANLkTi=4Ds3mMHepozgfjAe2W2Guj7GgJQ@mail.gmail.com>
References: <BANLkTi=4Ds3mMHepozgfjAe2W2Guj7GgJQ@mail.gmail.com>
Message-ID: <4D9E3A1F.8050306@dundee.ac.uk>

Dear Mihaly,

I am sorry for belated response. I'd suggest simplifying your plan a 
little. For example you do not need to write what you are going to do 
every day of GSoC. One week precision will be fine. On the other hand, 
it would be good to include formulas into the plan as well as expand the 
original idea with something that is in line with the project and 
interest you.

Did you have a go at the coding exercise? If not I would recommend you 
to do that.
Finally do not forget to send your proposal to melange.

Regards,
Peter


On 06/04/2011 21:35, Mihaly Cs?k?s wrote:
>
> Dear Peter,
>
> I am very interested in gsoc and I would like to apply for the BioJava 
> - Amino acids physico-chemical properties calculation project.
>
> I send you my Proposal in the attachment. Please if you have a little 
> time, read it throughand write me your opinion.
>
> Thank you in advance!
>
> Yours sincerely:
>
> Mihaly Csokas
>


From andreas at sdsc.edu  Fri Apr  8 00:45:41 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 7 Apr 2011 21:45:41 -0700
Subject: [Biojava-l] GSoC last day to submit proposals
Message-ID: <BANLkTikBWp4exPDaVnKAE6BeJ6kcyOiJiw@mail.gmail.com>

Hi,

This is the final reminder that the deadline for submitting proposals
for the Google Summer of Code is Friday April 8th, 19:00 UTC.

Andreas

From kohchuanhock at gmail.com  Fri Apr  8 13:46:21 2011
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Sat, 9 Apr 2011 01:46:21 +0800
Subject: [Biojava-l] Submission of Short Coding Exercise
Message-ID: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>

Dear Dr Peter Troshin,

I had completed the short coding exercise. As I was about to submit it, I
realize that I am unsure about the behavior that runme.jar should exhibit.

In Goal 2, it was given that the example command is "java FindEnds
inputFile.txt outputFile.txt"

Am I right to say that runme.jar should replace FindEnds and run as follows?

"java -jar runme.jar inputFile.txt outputFile.txt"

Please advice. Thanks.

Looking forward to your reply.

Regards,
Chuan Hock

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>

From p.v.troshin at dundee.ac.uk  Fri Apr  8 17:43:29 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Fri, 08 Apr 2011 22:43:29 +0100
Subject: [Biojava-l] Submission of Short Coding Exercise
In-Reply-To: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>
References: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>
Message-ID: <4D9F8181.9040204@dundee.ac.uk>

Hello Chuan,

Yes, you are right.

Peter

On 08/04/2011 18:46, Chuan Hock Koh wrote:
> Dear Dr Peter Troshin,
>
> I had completed the short coding exercise. As I was about to submit it, I
> realize that I am unsure about the behavior that runme.jar should exhibit.
>
> In Goal 2, it was given that the example command is "java FindEnds
> inputFile.txt outputFile.txt"
>
> Am I right to say that runme.jar should replace FindEnds and run as follows?
>
> "java -jar runme.jar inputFile.txt outputFile.txt"
>
> Please advice. Thanks.
>
> Looking forward to your reply.t.
>
> Regards,
> Chuan Hock
>


From khalil.elmazouari at gmail.com  Mon Apr 11 16:25:15 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Mon, 11 Apr 2011 22:25:15 +0200
Subject: [Biojava-l] RichSequenceIterator.hasNext from empty file return
	true!!!
Message-ID: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>

Hi,

RichSequenceIterator.hasNext from empty file return true!!! and throws an infinite BioException loop!!!
Any explanation?? Thanks

khalil

test using the following code

    public static void main(String[] args) {
       String path = "emptyFile.txt";

         BufferedReader br = null;
      try {
         br = new BufferedReader(new FileReader(path));
      } catch (FileNotFoundException ex) {
         ex.printStackTrace();
      }
      RichSequenceIterator seqs = RichSequence.IOTools.readFastaProtein(br, null);
        while (seqs.hasNext()) {
         try {
            RichSequence seq = seqs.nextRichSequence();
         } catch (NoSuchElementException ex) {
            ex.printStackTrace();
         } catch (BioException ex) {
            ex.printStackTrace();
         }
        }

====

org.biojava.bio.BioException: Could not read sequence
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at com.kem.ae.core.Empty.main(Empty.java:51)
Caused by: java.io.IOException: Premature stream end
        at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 1 more
org.biojava.bio.BioException: Could not read sequence
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at com.kem.ae.core.Empty.main(Empty.java:51)
Caused by: java.io.IOException: Premature stream end
        at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)

infinite loop....



From chapmanb at 50mail.com  Tue Apr 12 08:36:32 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 12 Apr 2011 08:36:32 -0400
Subject: [Biojava-l] Bioinformatics Open Source Conference (BOSC
 2011)--Abstracts due April 18th!
Message-ID: <20110412123632.GE2105@kunkel>

Only one week left to submit an abstract to BOSC 2011! We have
two great keynote speakers lined up (Lawrence Hunter and Matt
Wood) and session topics that include parallel and cloud-based
approaches to bioinformatics, genome content management, and tools for
next-generation sequencing. We'd love to hear about your Open Source
bioinformatics project!

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)
July 15-16, 2011, in Vienna, Austria
http://www.open-bio.org/wiki/BOSC_2011

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session 
  (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011. All students whose abstracts
are accepted for talks will be considered for this award.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice
(co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London,
Ron Taylor

From gwaldon at geneinfinity.org  Tue Apr 12 14:02:28 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 12 Apr 2011 13:02:28 -0500
Subject: [Biojava-l] RichSequenceIterator.hasNext from empty file return
 true!!!
In-Reply-To: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>
References: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>
Message-ID: <20110412130228.31866c2hd15fztm8@gator1273.hostgator.com>

Hi Khali,

In my hands I found "java.io.FileNotFoundException: emptyFile.txt (The  
system cannot find the file specified)", which is not exactly the same  
thing as an empty file. Anyway, I think you are right and  
RichStreamReader should switch the moreSequenceAvailable flag before  
throwing the exception. In your case just get out of the loop and you  
should be safe. Thanks for reporting.

George

Quoting Khalil El Mazouari <khalil.elmazouari at gmail.com>:

> Hi,
>
> RichSequenceIterator.hasNext from empty file return true!!! and  
> throws an infinite BioException loop!!!
> Any explanation?? Thanks
>
> khalil
>
> test using the following code
>
>     public static void main(String[] args) {
>        String path = "emptyFile.txt";
>
>          BufferedReader br = null;
>       try {
>          br = new BufferedReader(new FileReader(path));
>       } catch (FileNotFoundException ex) {
>          ex.printStackTrace();
>       }
>       RichSequenceIterator seqs =  
> RichSequence.IOTools.readFastaProtein(br, null);
>         while (seqs.hasNext()) {
>          try {
>             RichSequence seq = seqs.nextRichSequence();
>          } catch (NoSuchElementException ex) {
>             ex.printStackTrace();
>          } catch (BioException ex) {
>             ex.printStackTrace();
>          }
>         }
>
> ====
>
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>         ... 1 more
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>
> infinite loop....
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>




From mandarijnopw8 at gmail.com  Wed Apr 13 10:47:12 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Wed, 13 Apr 2011 16:47:12 +0200
Subject: [Biojava-l] GSOC
Message-ID: <4DA5B770.7040809@gmail.com>

Hi everyone,

i am student who would like to join GSOC with another programmer.
But we still are in need of a mentor who can guide us.

is there someone with biojava experience who can help us during GSOC?

greetings,
Shamanou van Leeuwen



From rmb32 at cornell.edu  Wed Apr 13 11:30:59 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 13 Apr 2011 08:30:59 -0700
Subject: [Biojava-l] last call for Google Summer of Code mentors
Message-ID: <4DA5C1B3.4010504@cornell.edu>

Hi all,

This is the last call for mentors for Google Summer of Code.  We have a 
good crop of student proposals this year for doing work on OBF projects, 
and money from Google to fund them, but we need experienced Bio* 
developers to mentor them.

If you'd like to see the student proposals, participate in their 
scoring, and possibly volunteer to mentor them (remotely of course) over 
the summer, do two things:

1.) Create an account on http://google-melange.com and send a request to 
be an admin from the OBF page on there, 
http://www.google-melange.com/gsoc/org/google/gsoc2011/obf

2.) Join the OBF GSoC mentors mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc-mentors

Even if you just want to see the student applications and help with 
scoring, but don't necessarily have time to mentor a student, your input 
in the scoring process is appreciated.  :-)

Rob

----
Robert Buels
OBF GSoC 2011 Administrator



From andreas at sdsc.edu  Wed Apr 13 23:17:29 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 13 Apr 2011 20:17:29 -0700
Subject: [Biojava-l] GSOC
In-Reply-To: <4DA5B770.7040809@gmail.com>
References: <4DA5B770.7040809@gmail.com>
Message-ID: <BANLkTi=AANj4tXqHegPF=SrVzqv9z0Wn+g@mail.gmail.com>

Hi Shamanou,

The deadline for submitting proposals was last Friday. Usually the
funding is for one student only and not for pairs of students...

Andreas

On Wed, Apr 13, 2011 at 7:47 AM, Shamanou van Leeuwen
<mandarijnopw8 at gmail.com> wrote:
> Hi everyone,
>
> i am student who would like to join GSOC with another programmer.
> But we still are in need of a mentor who can guide us.
>
> is there someone with biojava experience who can help us during GSOC?
>
> greetings,
> Shamanou van Leeuwen
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From p.v.troshin at dundee.ac.uk  Wed Apr  6 11:49:59 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 06 Apr 2011 16:49:59 +0100
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTinfMi-XDkqnnxrVnMqfjaLttHuEKQ@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>	<BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>	<4D99D6C2.9060107@dundee.ac.uk>
	<BANLkTinfMi-XDkqnnxrVnMqfjaLttHuEKQ@mail.gmail.com>
Message-ID: <4D9C8BA7.4020806@dundee.ac.uk>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110406/f1be172e/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: molecularweight.gif
Type: image/gif
Size: 1390 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110406/f1be172e/attachment-0001.gif>

From mostafa.shokrof at gmail.com  Thu Apr 14 07:35:57 2011
From: mostafa.shokrof at gmail.com (Mostafa Shokrof)
Date: Thu, 14 Apr 2011 13:35:57 +0200
Subject: [Biojava-l] Google summer code proposal
Message-ID: <BANLkTi=_tN87ukG9=LNgg5=+XdA94E+nSQ@mail.gmail.com>

On Thu, Apr 14, 2011 at 8:48 AM, Jason Stajich <jason.stajich at gmail.com>wrote:

> Mostafa -
>
> I may have accidently deleted your post to biojava-l about GSOC that was in
> the held queue for the mailiman system. If you can resend it to the list one
> more time I will make sure it goes through.
>
>
> Name :Mostafa EL-Sayed Shokrof
>
> Email:mostafa.shokrof at gmail.com
>
> Physical Address:7 el gomhoreya off tarh el bahr st - el shark -portsaid
> -Egypt
>
> Telephone Number:02-016755576
>
> I am a third year student in Bioinformatics department computer science
> faculty Ain shams university with average grade A. I am interested in
> applying for amino acid properties calculation project which-i do believe-
> is a great opportunity to enhance my experience. I chose Open-Bio
> organization as it offers interaction with real world Bioinformatics applications
> which would certainly help me a lot in my graduation project next semester.
> Choosing this project in particular was based on several reasons. Firstly I
> believe in the project's importance as it addresses core Bioinformatics
> problems and applies Bioinformatics algorithms..Second it will be
> implemented in Java ,which has two main advantages ,it is Object oriented
> and cross platform . ,so I think BIO-Java project is very useful.
>
> I also believe I am well suited for this project as I passed both
> Algorithms and OOP courses with grade A ,besides my strong background in
> biology as I studied biology and Bioinformatics at college.
>
> Not only did I gain my programming experience by attending training courses
> in CIT Global Mobi dev company for mobile applications last summer , but I
> also studied the following courses:
>
> 1.Structural Programming
>
> 2.Data Structure
>
> 3.OOP
>
> 4.Algorithms
>
> 5.File Organization
>
> 6.Software Engineering
>
> Courses being studied this semester are:
>
> 6.Numerical Analysis
>
> 7.System Analysis
>
>
>
> Concerning my biological background,I have studied:
>
> 1.Introduction to Biology
>
> 2.Introduction to Biochemistry
>
> 3.Introduction to Biophysics
>
> 4.Introduction to Molecular Cell Biology
>
> 5.Advanced Molecular Genetics
>
> 6.Introduction to Bioinformatics
>
> Courses being studied in this semester:
>
> 7.Biotechnology
>
> 8.Structural Bioinformatics
>
>
>
> Unfortunately Google schedule does not fit me since our exams are expected
> to be delayed due to the current circumstances in Egypt ,so I hope I will be
> free on the beginning of July .
>
> But after that I will dedicate my summer to GSCO .I can work an average 8
> hours a day ,five days a week of total 40 hours a week. The New semester
> starts at the half of September. so I will have plenty of time .Finally I
> would be really grateful if you provided me this cherish opportunity which
> would help me out in my career further on.
>
>
>
>
>
> I attached time line for the project ,UML design ,Abstract of how the
> implementation will look and , the Short code Exercise with the proposal,
>
> I will appreciate your feedback..
>
resourceshttps://
> docs.google.com/leaf?id=0B-lMAeKAGH9gYjFjNWFmZmItMGZkMC00NDIwLWFlODgtMDUzYzhlYWEwNzk0&hl=en:
>
>
> my regards,
>
> Mostafa Shokrof
>
> Bioinformatics student
> Ain Shams University
>

From erikclarke at gmail.com  Thu Apr 14 22:41:48 2011
From: erikclarke at gmail.com (Erik C)
Date: Thu, 14 Apr 2011 19:41:48 -0700
Subject: [Biojava-l] needleman-wunsch score problems
Message-ID: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>

Hi all,
I'm having some trouble reconciling the scores from the NeedlemanWunsch
sequence alignment object in BioJava with the scores I'm getting from the
EMBL-EBI command-line tool 'needle'. Specifically, for the same sequences,
matrix, and penalties, BioJava returns 274 (in one case), while `needle'
returns 163.
Does anybody have any ideas as to why this might be happening? Is there a
parameter or setting I'm missing? My implementation of the n.w. code in
biojava is below:

    public long alignTwoSequences(ProteinSequence subject,
            ProteinSequence target) {

        SubstitutionMatrix<AminoAcidCompound> blosum62 =
SubstitutionMatrixHelper.getBlosum62();
        GapPenalty penalties = new SimpleGapPenalty();
        penalties.setExtensionPenalty((short) .5);
        penalties.setOpenPenalty((short) 10);
        NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new
NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(subject, target,
penalties, blosum62);
        return nw.getScore();

    }

Thanks,
Erik

From andreas at sdsc.edu  Thu Apr 14 23:14:16 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 Apr 2011 20:14:16 -0700
Subject: [Biojava-l] needleman-wunsch score problems
In-Reply-To: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>
References: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>
Message-ID: <BANLkTimBKs0XZkfie9Jd-rGtZVkN+-DPkg@mail.gmail.com>

Hi Eric,

Did you compare the alignments, i.e which pairs of amino acids are
getting aligned? There might be subtle differences..

Andreas


On Thu, Apr 14, 2011 at 7:41 PM, Erik C <erikclarke at gmail.com> wrote:
> Hi all,
> I'm having some trouble reconciling the scores from the NeedlemanWunsch
> sequence alignment object in BioJava with the scores I'm getting from the
> EMBL-EBI command-line tool 'needle'. Specifically, for the same sequences,
> matrix, and penalties, BioJava returns 274 (in one case), while `needle'
> returns 163.
> Does anybody have any ideas as to why this might be happening? Is there a
> parameter or setting I'm missing? My implementation of the n.w. code in
> biojava is below:
>
> ? ?public long alignTwoSequences(ProteinSequence subject,
> ? ? ? ? ? ?ProteinSequence target) {
>
> ? ? ? ?SubstitutionMatrix<AminoAcidCompound> blosum62 =
> SubstitutionMatrixHelper.getBlosum62();
> ? ? ? ?GapPenalty penalties = new SimpleGapPenalty();
> ? ? ? ?penalties.setExtensionPenalty((short) .5);
> ? ? ? ?penalties.setOpenPenalty((short) 10);
> ? ? ? ?NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new
> NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(subject, target,
> penalties, blosum62);
> ? ? ? ?return nw.getScore();
>
> ? ?}
>
> Thanks,
> Erik
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jayunit100 at gmail.com  Fri Apr 15 13:16:18 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Fri, 15 Apr 2011 13:16:18 -0400
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
Message-ID: <BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>

I adopted a java Needlman Wunsch for proteins and it works fine ; if someone
wants to integrate it or integrate or compare it w/ biojava's implementation
i can provide it just email me i will send the source .

otherwise i can potentially just try to commit it to a sandbox repo if one
exists....

From andreas at sdsc.edu  Fri Apr 15 15:14:34 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 15 Apr 2011 12:14:34 -0700
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
Message-ID: <BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>

Hi Jay,

CCing the list again, somehow I dropped it off this thread.. If I
understand your example right, you want the alignment to only span the
domain that is share between the two proteins. This suggests you would
use a local alignment, not penalizing end gaps.. If you provide some
example IDs we can be more specific...

Andreas



On Fri, Apr 15, 2011 at 11:32 AM, JAX <jayunit100 at gmail.com> wrote:
> Thanks andreas : ?Is there a way to globally align to sequences using smith watermans optimal local alignment; I.e. So as to get an ideal alignment of two multi domain proteins (which only share one domain), that is gapped in such a way so as to cover the whole protein length?
>
> Sent from my iPad
>
> Sent from my iPad
>
> On Apr 15, 2011, at 2:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Jay,
>>
>> thanks for the suggestion. There is already a needleman wunsch and
>> smith waterman implementation available as part of the alignment
>> module. Have you seen those?
>>
>> http://biojava.org/wiki/BioJava:CookBook3:PSA
>>
>> Andreas
>>
>> On Fri, Apr 15, 2011 at 10:16 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
>>> I adopted a java Needlman Wunsch for proteins and it works fine ; if someone
>>> wants to integrate it or integrate or compare it w/ biojava's implementation
>>> i can provide it just email me i will send the source .
>>>
>>> otherwise i can potentially just try to commit it to a sandbox repo if one
>>> exists....
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>


From jayunit100 at gmail.com  Fri Apr 15 15:30:30 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Fri, 15 Apr 2011 15:30:30 -0400
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
	<BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
Message-ID: <BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>

Consider Kalirin , a multidomain protein.

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=NP_003938.1

Now, lets say I aligned Kalirin with a single domain member of the RHO-Gef
family....  Then only one part of the sequence would match....  But what if
I WANTED a global alignment, for programmatic purposes... Then I would want
an alignment like this

------------------------------------------------RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF------

With lots of gaps in the beggining, and lots of matches at the end, where
the length of the alignment between the two proteins was exactly equivalent.
 Contrast this with a smith waterman output, which would look like this :

RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF....

So is there a way to get the specificity of Smith Waterman in a Needlman
Wunsch alignment ?

From andreas at sdsc.edu  Fri Apr 15 17:49:36 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 15 Apr 2011 14:49:36 -0700
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
	<BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
	<BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>
Message-ID: <BANLkTimF+P-88=WGeCuOZR1paBF5ko2YTg@mail.gmail.com>

It sounds like you are talking about doing a needleman wunsch
alignment, while not penalizing end gaps. This should give you quite
similar results to just doing a
smith waterman one.

Is it the alignment display that you are concerned about? You could
easily fill up the ends with unaligned regions for smith waterman
results.  I don't find end-gaps particularly informative. Usually an
alignment display will give you the aligned positions, then you can
easily see (or script) if there are end gaps.

Hope that makes sense..
Andreas



On Fri, Apr 15, 2011 at 12:30 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Consider Kalirin , a multidomain protein.
> http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=NP_003938.1
> Now, lets say I aligned Kalirin with a single domain member of the RHO-Gef
> family.... ?Then only one part of the sequence would match.... ?But what if
> I WANTED a global alignment, for programmatic purposes... Then I would want
> an alignment like this
> ------------------------------------------------RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF------
> With lots of gaps in the beggining, and lots of matches at the end, where
> the length of the alignment between the two proteins was exactly equivalent.
> ?Contrast this with a smith waterman output, which would look like this :
> RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF....
> So is there a way to get the specificity of Smith Waterman in a Needlman
> Wunsch alignment ?


From Wim.DeSmet at UGent.be  Mon Apr 18 11:22:26 2011
From: Wim.DeSmet at UGent.be (Wim De Smet)
Date: Mon, 18 Apr 2011 17:22:26 +0200
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
Message-ID: <4DAC5732.5010507@UGent.be>

Hi all,

I've been trying to generate some global alignments with biojava and 
comparing them with what needle returns. Doing this, I can't seem to 
reproduce needle's alignment with biojava. The score returned from 
biojava seems to be worse than that from needle, so I'm not sure what's 
happening here.

The sequences are AB004720 and Y17238 (I didn't attach a fasta file to 
avoid spamming people, let me know if you want one). I align them with:
GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = 
Alignments.getPairwiseAligner(
new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
PairwiseSequenceAlignerType.GLOBAL,
penalty, SubstitutionMatrixHelper.getNuc4_4());
SequencePair<DNASequence, NucleotideCompound>
alignment = aligner.getPair();

This gives me an alignment with only 23% similarity and a gap at the 
end. Varying the gap penalties can give me a gap in front too, but 
that's about it. When aligning in needle, I get a sequence with a higher 
score (6784 vs (-)5862) and 94% similarity (which seems closer to home). 
Needle I just run with defaults (so it uses EDNAFULL) and a go/ge of 14/4.

Could this be a bug or am I misunderstanding some of the options?

BTW, if I use a really large gapextend, say -4000, I also get a 
nullpointer exception.

TIA,
Wim De Smet

-- 
Wim De Smet
http://www.straininfo.net/

From andreas at sdsc.edu  Mon Apr 18 14:34:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 18 Apr 2011 11:34:57 -0700
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <4DAC5732.5010507@UGent.be>
References: <4DAC5732.5010507@UGent.be>
Message-ID: <BANLkTinZuaB_vQ1iUDQshqY6k5sY7cu8LQ@mail.gmail.com>

Hi Wim,

thanks for tracking this down. I agree, something does not look right
here. I'll try to see what is going on...

Andreas

On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> Hi all,
>
> I've been trying to generate some global alignments with biojava and
> comparing them with what needle returns. Doing this, I can't seem to
> reproduce needle's alignment with biojava. The score returned from biojava
> seems to be worse than that from needle, so I'm not sure what's happening
> here.
>
> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
> spamming people, let me know if you want one). I align them with:
> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
> Alignments.getPairwiseAligner(
> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> PairwiseSequenceAlignerType.GLOBAL,
> penalty, SubstitutionMatrixHelper.getNuc4_4());
> SequencePair<DNASequence, NucleotideCompound>
> alignment = aligner.getPair();
>
> This gives me an alignment with only 23% similarity and a gap at the end.
> Varying the gap penalties can give me a gap in front too, but that's about
> it. When aligning in needle, I get a sequence with a higher score (6784 vs
> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>
> Could this be a bug or am I misunderstanding some of the options?
>
> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
> exception.
>
> TIA,
> Wim De Smet
>
> --
> Wim De Smet
> http://www.straininfo.net/
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From andreas at sdsc.edu  Wed Apr 20 13:33:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 20 Apr 2011 10:33:03 -0700
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <4DAC5732.5010507@UGent.be>
References: <4DAC5732.5010507@UGent.be>
Message-ID: <BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>

Hi Wim,

are you sure you are using the correct sequences in your test? When I
run the code at the bottom of this emails I am getting 95 and 97%
sequence ID, which is similar to what you are expecting.

Andreas

Here my code: (using latest code from SVN)

package demo;

import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SubstitutionMatrixHelper;
import org.biojava3.alignment.template.GapPenalty;
import org.biojava3.alignment.template.PairwiseSequenceAligner;
import org.biojava3.alignment.template.SequencePair;
import org.biojava3.core.sequence.DNASequence;
import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava3.core.sequence.compound.NucleotideCompound;

public class TestDNANeedlemanWunsch {
	public static void main(String[] args){

		String query =
"AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA"
+
		"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
		"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
		"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
		"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
		"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
		"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
		"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
		"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
		"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
		"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
		"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
		"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
		"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
		"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
		"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
		"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
		"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
		"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
		"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
		"CCCTTGTGGAGGGAGCCGGTAATTAAA";

		String target =
"CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC"
+
		"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
		"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
		"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
		"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
		"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
		"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
		"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
		"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
		"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
		"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
		"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
		"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
		"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
		"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
		"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
		"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
		"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
		"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
		"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
		"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";

		GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
Alignments.getPairwiseAligner(
				new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
				new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
				PairwiseSequenceAlignerType.GLOBAL,
				penalty, SubstitutionMatrixHelper.getNuc4_4());
		SequencePair<DNASequence, NucleotideCompound>
		alignment = aligner.getPair();
		
		System.out.println(alignment);
		
		int identical = alignment.getNumIdenticals();
		System.out.println("Number of identical residues: " + identical);
		System.out.println("% identical query: " + identical / (float)
query.length() );
		System.out.println("% identical query: " + identical / (float)
target.length() );
	}
}






On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> Hi all,
>
> I've been trying to generate some global alignments with biojava and
> comparing them with what needle returns. Doing this, I can't seem to
> reproduce needle's alignment with biojava. The score returned from biojava
> seems to be worse than that from needle, so I'm not sure what's happening
> here.
>
> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
> spamming people, let me know if you want one). I align them with:
> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
> Alignments.getPairwiseAligner(
> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> PairwiseSequenceAlignerType.GLOBAL,
> penalty, SubstitutionMatrixHelper.getNuc4_4());
> SequencePair<DNASequence, NucleotideCompound>
> alignment = aligner.getPair();
>
> This gives me an alignment with only 23% similarity and a gap at the end.
> Varying the gap penalties can give me a gap in front too, but that's about
> it. When aligning in needle, I get a sequence with a higher score (6784 vs
> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>
> Could this be a bug or am I misunderstanding some of the options?
>
> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
> exception.
>
> TIA,
> Wim De Smet
>
> --
> Wim De Smet
> http://www.straininfo.net/
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From jayunit100 at gmail.com  Wed Apr 20 13:54:44 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Wed, 20 Apr 2011 13:54:44 -0400
Subject: [Biojava-l] biojava resolver issues in maven
Message-ID: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>

   Hi guys, I've intermittently been getting some weird biojava/maven
resolution errors.  Any ideas on this ?

4/20/11 1:52:13 PM EDT: [WARN] Failure to transfer
org.biojava:biojava3-structure:3.0-alpha3-SNAPSHOT/maven-metadata.xml from
http://download.java.net/maven/1 was cached in the local repository,
resolution will not be reattempted until the update interval of
maven-repository.dev.java.net has elapsed or updates are forced.

From andreas at sdsc.edu  Wed Apr 20 14:04:38 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 20 Apr 2011 11:04:38 -0700
Subject: [Biojava-l] biojava resolver issues in maven
In-Reply-To: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>
References: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>
Message-ID: <BANLkTikD1MGD5EDOt9fXZms4qfbpVKHzwQ@mail.gmail.com>

BioJava jar files are hosted at our own repository, not the public
Maven ones. It should be in your list of repositories, however if you
are setting up your own custom pom file, make sure to add:

<repositories>
 ...
	<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
</repositories>

Andreas

On Wed, Apr 20, 2011 at 10:54 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> ? Hi guys, I've intermittently been getting some weird biojava/maven
> resolution errors. ?Any ideas on this ?
>
> 4/20/11 1:52:13 PM EDT: [WARN] Failure to transfer
> org.biojava:biojava3-structure:3.0-alpha3-SNAPSHOT/maven-metadata.xml from
> http://download.java.net/maven/1 was cached in the local repository,
> resolution will not be reattempted until the update interval of
> maven-repository.dev.java.net has elapsed or updates are forced.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------


From frieman6 at gmail.com  Thu Apr 21 02:44:02 2011
From: frieman6 at gmail.com (omer f)
Date: Thu, 21 Apr 2011 09:44:02 +0300
Subject: [Biojava-l] Bio Java API - Amino Acids Data
Message-ID: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>

Hi All,

I Applied to the "Amino Acid" Project,
I found in the Bio Java API there is Amino Acids Objects,
But what i couldn't find - where there is Data (weight,Charge...) about each
Amino Acid,
My question, is there basic Data base for Amino Acids or we should get it
from user input,

Thank you,
Omer.

From Wim.DeSmet at UGent.be  Thu Apr 21 03:54:56 2011
From: Wim.DeSmet at UGent.be (Wim De Smet)
Date: Thu, 21 Apr 2011 09:54:56 +0200
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>
References: <4DAC5732.5010507@UGent.be>
	<BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>
Message-ID: <4DAFE2D0.7090601@UGent.be>

Hi Andreas

Thanks for having a look. I found the issue: if your sequence is lower 
case, the alignment is different. Try aligning with query.toLowerCase() 
and target.toLowerCase(), then the output is:

Number of identical residues: 334
% identical query: 0.23405746
% identical query: 0.22845417

vs upper case

Number of identical residues: 1394
% identical query: 0.9768746
% identical query: 0.95348835

So I just inserted a toUpperCase() and it works now.

Regards
Wim

On 20-04-11 19:33, Andreas Prlic wrote:
> Hi Wim,
>
> are you sure you are using the correct sequences in your test? When I
> run the code at the bottom of this emails I am getting 95 and 97%
> sequence ID, which is similar to what you are expecting.
>
> Andreas
>
> Here my code: (using latest code from SVN)
>
> package demo;
>
> import org.biojava3.alignment.Alignments;
> import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
> import org.biojava3.alignment.SimpleGapPenalty;
> import org.biojava3.alignment.SubstitutionMatrixHelper;
> import org.biojava3.alignment.template.GapPenalty;
> import org.biojava3.alignment.template.PairwiseSequenceAligner;
> import org.biojava3.alignment.template.SequencePair;
> import org.biojava3.core.sequence.DNASequence;
> import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
> import org.biojava3.core.sequence.compound.NucleotideCompound;
>
> public class TestDNANeedlemanWunsch {
> 	public static void main(String[] args){
>
> 		String query =
> "AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA"
> +
> 		"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
> 		"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
> 		"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
> 		"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
> 		"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
> 		"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
> 		"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
> 		"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
> 		"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
> 		"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
> 		"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
> 		"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
> 		"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
> 		"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
> 		"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
> 		"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
> 		"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
> 		"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
> 		"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
> 		"CCCTTGTGGAGGGAGCCGGTAATTAAA";
>
> 		String target =
> "CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC"
> +
> 		"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
> 		"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
> 		"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
> 		"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
> 		"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
> 		"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
> 		"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
> 		"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
> 		"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
> 		"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
> 		"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
> 		"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
> 		"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
> 		"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
> 		"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
> 		"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
> 		"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
> 		"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
> 		"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
> 		"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";
>
> 		GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> 		PairwiseSequenceAligner<DNASequence, NucleotideCompound>  aligner =
> Alignments.getPairwiseAligner(
> 				new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> 				new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> 				PairwiseSequenceAlignerType.GLOBAL,
> 				penalty, SubstitutionMatrixHelper.getNuc4_4());
> 		SequencePair<DNASequence, NucleotideCompound>
> 		alignment = aligner.getPair();
> 		
> 		System.out.println(alignment);
> 		
> 		int identical = alignment.getNumIdenticals();
> 		System.out.println("Number of identical residues: " + identical);
> 		System.out.println("% identical query: " + identical / (float)
> query.length() );
> 		System.out.println("% identical query: " + identical / (float)
> target.length() );
> 	}
> }
>
>
>
>
>
>
> On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet<Wim.DeSmet at ugent.be>  wrote:
>> Hi all,
>>
>> I've been trying to generate some global alignments with biojava and
>> comparing them with what needle returns. Doing this, I can't seem to
>> reproduce needle's alignment with biojava. The score returned from biojava
>> seems to be worse than that from needle, so I'm not sure what's happening
>> here.
>>
>> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
>> spamming people, let me know if you want one). I align them with:
>> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
>> PairwiseSequenceAligner<DNASequence, NucleotideCompound>  aligner =
>> Alignments.getPairwiseAligner(
>> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
>> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
>> PairwiseSequenceAlignerType.GLOBAL,
>> penalty, SubstitutionMatrixHelper.getNuc4_4());
>> SequencePair<DNASequence, NucleotideCompound>
>> alignment = aligner.getPair();
>>
>> This gives me an alignment with only 23% similarity and a gap at the end.
>> Varying the gap penalties can give me a gap in front too, but that's about
>> it. When aligning in needle, I get a sequence with a higher score (6784 vs
>> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
>> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>>
>> Could this be a bug or am I misunderstanding some of the options?
>>
>> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
>> exception.
>>
>> TIA,
>> Wim De Smet
>>
>> --
>> Wim De Smet
>> http://www.straininfo.net/
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>


-- 
Wim De Smet
http://www.straininfo.net/

From khalil.elmazouari at gmail.com  Thu Apr 21 06:36:29 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 12:36:29 +0200
Subject: [Biojava-l] Codon count
Message-ID: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>

Hi,

I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.

Any suggestion is welcome. 

Regards,

khalil




From ayates at ebi.ac.uk  Thu Apr 21 07:18:55 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:18:55 +0100
Subject: [Biojava-l] Bio Java API - Amino Acids Data
In-Reply-To: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>
References: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>
Message-ID: <4408CC30-6456-4269-B192-E9F66CEDAC3C@ebi.ac.uk>

Hi Omer,

If you are using BioJava3 then weight is available from the AminoAcidCompound object when taken from an AminoAcidCompoundSet. The other data points are not available from within BioJava. I know Andreas mentioned ages ago linking into one of the compound databases e.g. ChEBI but I don't think that's been done.

Regards,

Andy

On 21 Apr 2011, at 07:44, omer f wrote:

> Hi All,
> 
> I Applied to the "Amino Acid" Project,
> I found in the Bio Java API there is Amino Acids Objects,
> But what i couldn't find - where there is Data (weight,Charge...) about each
> Amino Acid,
> My question, is there basic Data base for Amino Acids or we should get it
> from user input,
> 
> Thank you,
> Omer.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From ayates at ebi.ac.uk  Thu Apr 21 07:23:47 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:23:47 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
Message-ID: <C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>

Hi Khalil,

I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.

Regards,

Andy

On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:

> Hi,
> 
> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
> 
> Any suggestion is welcome. 
> 
> Regards,
> 
> khalil
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From khalil.elmazouari at gmail.com  Thu Apr 21 07:37:16 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 13:37:16 +0200
Subject: [Biojava-l] Codon count
In-Reply-To: <C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
Message-ID: <1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>

Thanks Andy,
it's the second option I am looking for.

Regards,
khalil



On 21 Apr 2011, at 13:23, Andy Yates wrote:

> Hi Khalil,
> 
> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
> 
> Regards,
> 
> Andy
> 
> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
> 
>> Hi,
>> 
>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>> 
>> Any suggestion is welcome. 
>> 
>> Regards,
>> 
>> khalil
>> 
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 



From ayates at ebi.ac.uk  Thu Apr 21 07:40:00 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:40:00 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
Message-ID: <6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>

Hi Khalil,

Then I think windowed sequence is the only way to go. Actually one particularly "interesting" idea has just sprung to mind. What if you translated the entire sequence in frame 1 forward & reverse? Then finding the amount of correct codons is a case of looking for amino acids which are not a stop or unknown amino acid.

Andy

On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:

> Thanks Andy,
> it's the second option I am looking for.
> 
> Regards,
> khalil
> 
> 
> 
> On 21 Apr 2011, at 13:23, Andy Yates wrote:
> 
>> Hi Khalil,
>> 
>> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
>> 
>> Regards,
>> 
>> Andy
>> 
>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>> 
>>> Hi,
>>> 
>>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>>> 
>>> Any suggestion is welcome. 
>>> 
>>> Regards,
>>> 
>>> khalil
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> -- 
>> Andrew Yates                   Ensembl Genomes Engineer
>> EMBL-EBI                       Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>> 
>> 
>> 
>> 
> 

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From khalil.elmazouari at gmail.com  Thu Apr 21 07:54:23 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 13:54:23 +0200
Subject: [Biojava-l] Codon count
In-Reply-To: <6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
	<6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
Message-ID: <7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>

Hi Andy,

I am actually counting codons via 6 ORFs translations. I am working on ?100.000 seq/run => 600.000 ORFs to check. So, performance is an issue for my job.

I am just wondering if counting Codons directly on NT seq (both strand) will be faster vs translation + AA counting.

Regards,

khalil


On 21 Apr 2011, at 13:40, Andy Yates wrote:

> Hi Khalil,
> 
> Then I think windowed sequence is the only way to go. Actually one particularly "interesting" idea has just sprung to mind. What if you translated the entire sequence in frame 1 forward & reverse? Then finding the amount of correct codons is a case of looking for amino acids which are not a stop or unknown amino acid.
> 
> Andy
> 
> On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:
> 
>> Thanks Andy,
>> it's the second option I am looking for.
>> 
>> Regards,
>> khalil
>> 
>> 
>> 
>> On 21 Apr 2011, at 13:23, Andy Yates wrote:
>> 
>>> Hi Khalil,
>>> 
>>> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
>>> 
>>> Regards,
>>> 
>>> Andy
>>> 
>>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>>>> 
>>>> Any suggestion is welcome. 
>>>> 
>>>> Regards,
>>>> 
>>>> khalil
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>>> -- 
>>> Andrew Yates                   Ensembl Genomes Engineer
>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>> 
>>> 
>>> 
>>> 
>> 
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 



From ayates at ebi.ac.uk  Thu Apr 21 08:06:35 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 13:06:35 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
	<6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
	<7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>
Message-ID: <6177ca65-9f8b-40bb-8856-03bf6ad62361@email.android.com>

There will be a performance hit but you'll be rewriting the translation code so maybe the speed reduction isn't worth the recoding task. Give it a benchmark before recoding. I can't remember the exact speed but it isn't too slow

Andy

Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:

>Hi Andy,
>
>I am actually counting codons via 6 ORFs translations. I am working on
>?100.000 seq/run => 600.000 ORFs to check. So, performance is an issue
>for my job.
>
>I am just wondering if counting Codons directly on NT seq (both strand)
>will be faster vs translation + AA counting.
>
>Regards,
>
>khalil
>
>
>On 21 Apr 2011, at 13:40, Andy Yates wrote:
>
>> Hi Khalil,
>> 
>> Then I think windowed sequence is the only way to go. Actually one
>particularly "interesting" idea has just sprung to mind. What if you
>translated the entire sequence in frame 1 forward & reverse? Then
>finding the amount of correct codons is a case of looking for amino
>acids which are not a stop or unknown amino acid.
>> 
>> Andy
>> 
>> On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:
>> 
>>> Thanks Andy,
>>> it's the second option I am looking for.
>>> 
>>> Regards,
>>> khalil
>>> 
>>> 
>>> 
>>> On 21 Apr 2011, at 13:23, Andy Yates wrote:
>>> 
>>>> Hi Khalil,
>>>> 
>>>> I'm not 100% sure what you want here. If you just want to know the
>potential number of codons on both strands of DNA then it would be
>(length / 3)*2. If what you are actually asking for is how many codons
>code for an amino acid then you would have to perform work similar to
>the transcription engine in BJ3. All codon tables are available from
>the IUPACParser class & then it would be up to you to use a
>WindowedSequence over the top of your NT sequence to get the windows or
>SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the
>WindowedSequence.
>>>> 
>>>> Regards,
>>>> 
>>>> Andy
>>>> 
>>>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I am looking for a simple method or class to count the number of a
>specific AA codon on NT seq. Counting on both strands.
>>>>> 
>>>>> Any suggestion is welcome. 
>>>>> 
>>>>> Regards,
>>>>> 
>>>>> khalil
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>>> -- 
>>>> Andrew Yates                   Ensembl Genomes Engineer
>>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>> 
>> -- 
>> Andrew Yates                   Ensembl Genomes Engineer
>> EMBL-EBI                       Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>> 
>> 
>> 
>> 


From flf.mib at gmail.com  Thu Apr 21 17:18:01 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Thu, 21 Apr 2011 23:18:01 +0200
Subject: [Biojava-l] translation and leucine
Message-ID: <4DB09F09.4060303@gmail.com>

Dear all,
i have a quick question about translation with biojava 3

I would like to retrieve that the codon CTA is coding for a leucine.
But some leucine codons code also for a start in Universal Genetic code

Here I have build a very short example:
given  a short dna sequence coomposed of a start codon and 6 leucine codons

TranscriptionEngine e = TranscriptionEngine.getDefault();
DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
//return MLLLLLL : OK

DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
//return MLLLLLL : KO I would prefer have LLLLLLL !

DNASequence dd = new DNASequence("CTA");
//return M : KO I would prefer have L !

Could someone explain me this feature ?
How the default transcritionEngine works?

How can I ask to the TranscriptionEngine give me the aminoacids 
corresponding to CTA when it is not in first position?

Thanks a lot for your help !

Francois


From ayates at ebi.ac.uk  Thu Apr 21 17:46:14 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 22:46:14 +0100
Subject: [Biojava-l] translation and leucine
In-Reply-To: <4DB09F09.4060303@gmail.com>
References: <4DB09F09.4060303@gmail.com>
Message-ID: <44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>

Hi Francois,

The engine by default will always return the first amino acid as an init met if the amino acid could have been a start codon (but stupid atmo but it will be altered). If you do not want this behaviour then you'll have to create your own. You can do this using the following:

TranscriptionEngine e = new TranscriptionEngine.Builder().initMet(false).build();

HTH,

Andy

On 21 Apr 2011, at 22:18, Fran?ois Le F?vre wrote:

> Dear all,
> i have a quick question about translation with biojava 3
> 
> I would like to retrieve that the codon CTA is coding for a leucine.
> But some leucine codons code also for a start in Universal Genetic code
> 
> Here I have build a very short example:
> given  a short dna sequence coomposed of a start codon and 6 leucine codons
> 
> TranscriptionEngine e = TranscriptionEngine.getDefault();
> DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
> //return MLLLLLL : OK
> 
> DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
> //return MLLLLLL : KO I would prefer have LLLLLLL !
> 
> DNASequence dd = new DNASequence("CTA");
> //return M : KO I would prefer have L !
> 
> Could someone explain me this feature ?
> How the default transcritionEngine works?
> 
> How can I ask to the TranscriptionEngine give me the aminoacids corresponding to CTA when it is not in first position?
> 
> Thanks a lot for your help !
> 
> Francois
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/






From flf.mib at gmail.com  Sat Apr 23 02:12:53 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Sat, 23 Apr 2011 08:12:53 +0200
Subject: [Biojava-l] translation and leucine
In-Reply-To: <44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>
References: <4DB09F09.4060303@gmail.com>
	<44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>
Message-ID: <4DB26DE5.8000805@gmail.com>

Andy
ok, perfect I did not know it!
Thanks
Francois
> Hi Francois,
>
> The engine by default will always return the first amino acid as an init met if the amino acid could have been a start codon (but stupid atmo but it will be altered). If you do not want this behaviour then you'll have to create your own. You can do this using the following:
>
> TranscriptionEngine e = new TranscriptionEngine.Builder().initMet(false).build();
>
> HTH,
>
> Andy
>
> On 21 Apr 2011, at 22:18, Fran?ois Le F?vre wrote:
>
>> Dear all,
>> i have a quick question about translation with biojava 3
>>
>> I would like to retrieve that the codon CTA is coding for a leucine.
>> But some leucine codons code also for a start in Universal Genetic code
>>
>> Here I have build a very short example:
>> given  a short dna sequence coomposed of a start codon and 6 leucine codons
>>
>> TranscriptionEngine e = TranscriptionEngine.getDefault();
>> DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
>> //return MLLLLLL : OK
>>
>> DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
>> //return MLLLLLL : KO I would prefer have LLLLLLL !
>>
>> DNASequence dd = new DNASequence("CTA");
>> //return M : KO I would prefer have L !
>>
>> Could someone explain me this feature ?
>> How the default transcritionEngine works?
>>
>> How can I ask to the TranscriptionEngine give me the aminoacids corresponding to CTA when it is not in first position?
>>
>> Thanks a lot for your help !
>>
>> Francois
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l


From rmb32 at cornell.edu  Mon Apr 25 17:42:48 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 25 Apr 2011 14:42:48 -0700
Subject: [Biojava-l] Announcing OBF Google Summer of Code Accepted Students
Message-ID: <4DB5EAD8.1020905@cornell.edu>

Hello all,

I'm very pleased and excited to announce that the Open Bioinformatics 
Foundation has selected 6 very capable students to work on OBF projects 
this summer as part of the Google Summer of Code program.

The accepted students, their projects, and their mentors (in 
alphabetical order):

Justinas Vygintas Daugmaudis
Michele dos Santos da Silva
    (2 students!)
    Mocapy++Biopython: from data to probabilistic models of biomolecules
    mentored by Thomas Hamelryck and Eric Talevich

Chuan Hock Koh
   BioJava - Amino acids physico-chemical properties calculation
   mentored by Peter Troshin, Andreas Prlic, and Jay Vyas

Micha? Koziarski
    Representing bio-objects and related information with images
    (BioRuby)
    mentored by Raoul J.P. Bonnal and Francesco Strozzi

Sheena Scroggins
    Major BioPerl Reorganization
    mentored by Robert Buels and Chris Fields

Mikael Eric Trellet
    Interface analysis module for BioPython
    mentored by Jo?o Rodrigues and Eric Talevich


Once again this year, we received many great applications and ideas. 
However, funding and mentor resources are limited, and we were not able 
to accept as many as we would have liked.  Our deepest thanks to all the 
students who applied: we sincerely appreciate the time and effort you 
put into your applications, and hope you will still consider being a 
part of the OBF's open source projects, even without Google funding.  I 
speak for myself and all of the mentors who read and scored applications 
when I say that we were truly honored by the number and quality of the 
applications we received.

For the accepted students: congratulations!  You have risen to the top 
of a very competitive application process.  Now it's time to "put your 
money where your mouth is", as the saying goes.  Let's get out there and 
write some great code this summer!

Best regards,

Rob

----
Robert Buels
OBF GSoC 2011 Administrator

From pavlo.lutsik at googlemail.com  Tue Apr 26 07:07:42 2011
From: pavlo.lutsik at googlemail.com (Pavlo Lutsik)
Date: Tue, 26 Apr 2011 13:07:42 +0200
Subject: [Biojava-l] NCBIQBlastService
Message-ID: <op.vujk64qq4c6xo5@plus-laptop-win.funklan.uni-saarland.de>


Hi,

cannot get the subject class working in the Cookbook example. Simple  
rbw.printRemoteBlastInfo() throws the

java.lang.Exception: Impossible to get info from QBlast service at this  
time. Check your network connection.

Any ideas?

Best,
Pavlo Lutsik

From p.v.troshin at dundee.ac.uk  Wed Apr 27 09:49:54 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 27 Apr 2011 14:49:54 +0100
Subject: [Biojava-l] amino acid physico-chemical properties calculation
	project
In-Reply-To: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
References: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
Message-ID: <4DB81F02.2020504@dundee.ac.uk>

Dear students,

I would like to thank all of you for your interest in and enthusiasm for 
the amino acid physico-chemical properties calculation project 2011 
Google Summer of Code. Unfortunately, only one student has to be chosen 
and I am sorry if this happens not to be you.

This idea generated enormous interest and we have received a total of 18 
applications for this idea. Many of those are of good or very good 
quality. I worked with many of you during the application process, and 
was very impressed by the level of enthusiasm, energy, and capability I 
saw in the applications and our conversations on the mailing list.

It wasn't easy to choose the best applicant, but we had to do it.

A few general comments on the solutions for the short coding exercise.

1) Make sure you understand the task. About half of the application 
fails to stick to the specifications.

2) Only a few people used threads correctly. Among them only one person 
used java.concurrency package, which I expected everyone to use. I would 
recommend reading B.Goetz "Java Concurrency in Practice" if you want to 
learn more about multithreading in Java.

3) Do not overcomplicate the solution; good programmer would do just 
what he was asked to.

4) You can determine whether your solution worked correctly by 
processing the following input

aaabbbccc    bbcccalkfw
aaaabb    aaabbbcc
caaabbbccc    aaabbbccc
aaaaabbbbb    abbbbbccdddd
sjdhfjksdhfk    weiuriweiru
ddddrepeatrepeat    repeatrepeat

and comparing it to the output that should have been produced:

aaab
a
c
aaaa
sjdhfjksdhfk
dddd

Thanks to everyone again, and I wish you all the best of luck with 
whatever endeavour you take on.

Regards,
Peter




On 26/04/2011 07:33, Alexandru Paiu wrote:
>  Hi Peter .
>
>  I want to know what should I improve in the next gsoc . I wan't to
>  know what wasn't right for my application .
>
>  In my opinion I think that I did a good job with the solutions for
>  instability index and isoelectric point which are the hardest methods
>  . I even used the jay vyas suggestion with those hashtables .
>
>  Please , give me an advice
>
>  Best regards Paiu Alexandru



From p.v.troshin at dundee.ac.uk  Wed Apr 27 10:05:42 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 27 Apr 2011 15:05:42 +0100
Subject: [Biojava-l] Please give me an advice
In-Reply-To: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
References: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
Message-ID: <4DB822B6.9030003@dundee.ac.uk>

Dear Alex,

There was nothing particularly wrong with your project plan, it just was 
not as good as the winning proposal. Your solution for the coding 
exercise did not run out of the box (java -jar runme.jar), was not 
correct and could have been better engineered.

I'd recommend you to contribute to the open source project of your 
choice before applying to the GSoC next year. This way you will be in a 
much better position for the next GSoC.

Regards,
Peter

On 26/04/2011 07:33, Alexandru Paiu wrote:
> Hi Peter .
>
> I want to know what should I improve in the next gsoc . I wan't to 
> know what wasn't right for my application .
>
> In my opinion I think that I did a good job with the solutions for 
> instability index and isoelectric point which are the hardest methods 
> . I even used the jay vyas suggestion with those hashtables .
>
> Please , give me an advice
>
> Best regards
> Paiu Alexandru


From flf.mib at gmail.com  Wed Apr 27 15:54:28 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Wed, 27 Apr 2011 21:54:28 +0200
Subject: [Biojava-l] biojava3 and blast xml parser
Message-ID: <4DB87474.1080307@gmail.com>

Dear all,

I have just a difficulty: is there still a blast xml parser in the 
biojava 3.0-SNAPSHOT
I am not able to find it...

I have found
http://www.biojava.org/docs/api1.8/org/biojava/bio/program/sax/blastxml/BlastXMLParser.html
with a good tutorial here
http://biojava.org/wiki/BioJava:CookBook:Blast:Echo

but it seems to be part of biojava 1.8

can you confirm me?

Thanks

Francois


From willishf at ufl.edu  Wed Apr 27 17:30:52 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Wed, 27 Apr 2011 17:30:52 -0400
Subject: [Biojava-l] biojava3 and blast xml parser
In-Reply-To: <4DB87474.1080307@gmail.com>
References: <4DB87474.1080307@gmail.com>
Message-ID: <BANLkTimozSz2U4pV6sDj=WfvkfPmspgZ=w@mail.gmail.com>

We did not migrate the blast xml parser from 1.8 to 3.0. Typically I
will load the XML as a DOM object and use xpath to query the desired
results. I have some code in the biojava3-genome module
(org.biojava3.genome.BlastXMLQuery) that could possibly provide a
solution for you depending on what you are trying to accomplish. Let
me know if you have specific requirements that could help motivate
formal blast XML->Java objects support in Biojava3.

Thanks

Scooter

2011/4/27 Fran?ois Le F?vre <flf.mib at gmail.com>:
> Dear all,
>
> I have just a difficulty: is there still a blast xml parser in the biojava
> 3.0-SNAPSHOT
> I am not able to find it...
>
> I have found
> http://www.biojava.org/docs/api1.8/org/biojava/bio/program/sax/blastxml/BlastXMLParser.html
> with a good tutorial here
> http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
>
> but it seems to be part of biojava 1.8
>
> can you confirm me?
>
> Thanks
>
> Francois
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From gwaldon at geneinfinity.org  Sat Apr  2 00:11:02 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Fri, 01 Apr 2011 19:11:02 -0500
Subject: [Biojava-l] Expasy pI calculation algorythm
Message-ID: <20110401191102.44902rooroy3x9k4@gator1273.hostgator.com>

Hello,

Sorry if this comes a bit late; we had to solve some email issues -  
Thanks again to Andreas for doing it.

This is part of the email exchange I had with Christine Hoogland and  
Gregoire Rossier a few years ago regarding the algorithm used by  
"Compute pI/Mw" on the Expazy server. The code which was given to me  
is included at the end of this email; I used it to update bj1.

Good luck to all GSoC candidates,

George


On Tue, May 22, 2007 at 9:26 AM, Christine Hoogland via RT  
<tools at expasy.org> wrote:

     Dear George,

     Please find enclosed the algorithm we are using on ExPASy.

     I hope this helps.

     Best regards
     Christine

     >
     > The pK values used for "Compute pI/Mw" can be found in
     >
     > # Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
     > Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing
     > positions of polypeptides in immobilized pH gradients can be predicted
     > from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
     >
     > MEDLINE: 8125050
     >
     > # Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference
     > points
     > for comparisons of two-dimensional maps of proteins from different
     > human
     > cell types defined in a pH scale where isoelectric points correlate
     > with
     > polypeptide compositions. Electrophoresis 1994, 15, 529-539.
     >
     > MEDLINE: 8055880
     >
     > The pK were defined by examining polypeptide migration between pH 4.5
     > to
     > 7.3 in an immobilised pH gradient gel environment with 9.2M and 9.8M
     > urea at 15?C or 25?C. Prediction of protein pI for highly basic
     > proteins
     > is yet to be studied and it is possible that current Compute pI/Mw
     > predictions may not be adequate for this purpose.
     >
     > I hope this helps.
     >
     >
     > Best regards
     > Gregoire Rossier
     >
     >

     --------------------------------------------------------
     Christine Hoogland
     Swiss Institute of Bioinformatics
     CMU - 1, rue Michel Servet      Tel. (+41 22) 379 58 28
     CH - 1211 Geneva 4 Switzerland  Fax  (+41 22) 379 58 58
     Christine.Hoogland at isb-sib.ch   http://www.expasy.org/
     --------------------------------------------------------

     //  VERSION      :   1.6
     //  DATE         :   1/25/95
     //  Copyright 1993 by Swiss Institute of Bioinformatics. All  
rights reserved.

     //
     // Table of pk values :
     //  Note: the current algorithm does not use the last two columns. Each
     //  row corresponds to an amino acid starting with Ala. J, O and U are
     //  inexistant, but here only in order to have the complete alphabet.
     //
     //     Ct    Nt   Sm     Sc     Sn
     //

     static double cPk[26][5] = {
     3.55, 7.59, 0.   , 0.   , 0.    , // A
     3.55, 7.50, 0.   , 0.   , 0.    , // B
     3.55, 7.50, 9.00 , 9.00 , 9.00  , // C
     4.55, 7.50, 4.05 , 4.05 , 4.05  , // D
     4.75, 7.70, 4.45 , 4.45 , 4.45  , // E
     3.55, 7.50, 0.   , 0.   , 0.    , // F
     3.55, 7.50, 0.   , 0.   , 0.    , // G
     3.55, 7.50, 5.98 , 5.98 , 5.98  , // H
     3.55, 7.50, 0.   , 0.   , 0.    , // I
     0.00, 0.00, 0.   , 0.   , 0.    , // J
     3.55, 7.50, 10.00, 10.00, 10.00 , // K
     3.55, 7.50, 0.   , 0.   , 0.    , // L
     3.55, 7.00, 0.   , 0.   , 0.    , // M
     3.55, 7.50, 0.   , 0.   , 0.    , // N
     0.00, 0.00, 0.   , 0.   , 0.    , // O
     3.55, 8.36, 0.   , 0.   , 0.    , // P
     3.55, 7.50, 0.   , 0.   , 0.    , // Q
     3.55, 7.50, 12.0 , 12.0 , 12.0  , // R
     3.55, 6.93, 0.   , 0.   , 0.    , // S
     3.55, 6.82, 0.   , 0.   , 0.    , // T
     0.00, 0.00, 0.   , 0.   , 0.    , // U
     3.55, 7.44, 0.   , 0.   , 0.    , // V
     3.55, 7.50, 0.   , 0.   , 0.    , // W
     3.55, 7.50, 0.   , 0.   , 0.    , // X
     3.55, 7.50, 10.00, 10.00, 10.00 , // Y
     3.55, 7.50, 0.   , 0.   , 0.    }; // Z

     #define PH_MIN 0 /* minimum pH value */
     #define PH_MAX 14 /* maximum pH value */
     #define MAXLOOP 2000 /* maximum number of iterations */
     #define EPSI 0.0001 /* desired precision */

       //
       // Compute the amino-acid composition.
       //
       for (i = 0; i < sequenceLength; i++)
         comp[sequence[i] - 'A']++;

       //
       // Look up N-terminal and C-terminal residue.
       //
       nTermResidue = sequence[0] - 'A';
       cTermResidue = sequence[sequenceLength - 1] - 'A';

       phMin = PH_MIN;
       phMax = PH_MAX;

       for (i = 0, charge = 1.0; i < MAXLOOP && (phMax - phMin) > EPSI; i++)
         {
           phMid = phMin + (phMax - phMin) / 2;

           cter = exp10(-cPk[cTermResidue][0]) /
      (exp10(-cPk[cTermResidue][0]) + exp10(-phMid));
           nter = exp10(-phMid) /
      (exp10(-cPk[nTermResidue][1]) + exp10(-phMid));

           carg = comp[R] * exp10(-phMid) /
      (exp10(-cPk[R][2]) + exp10(-phMid));
           chis = comp[H] * exp10(-phMid) /
      (exp10(-cPk[H][2]) + exp10(-phMid));
           clys = comp[K] * exp10(-phMid) /
      (exp10(-cPk[K][2]) + exp10(-phMid));

           casp = comp[D] * exp10(-cPk[D][2]) /
      (exp10(-cPk[D][2]) + exp10(-phMid));
           cglu = comp[E] * exp10(-cPk[E][2]) /
      (exp10(-cPk[E][2]) + exp10(-phMid));

           ccys = comp[C] * exp10(-cPk[C][2]) /
      (exp10(-cPk[C][2]) + exp10(-phMid));
           ctyr = comp[Y] * exp10(-cPk[Y][2]) /
      (exp10(-cPk[Y][2]) + exp10(-phMid));

           charge = carg + clys + chis + nter -
      (casp + cglu + ctyr + ccys + cter);

           if (charge > 0.0)
              phMin = phMid;
           else
              phMax = phMid;
         }
       }




From frieman6 at gmail.com  Mon Apr  4 12:59:50 2011
From: frieman6 at gmail.com (omer f)
Date: Mon, 4 Apr 2011 15:59:50 +0300
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
Message-ID: <BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>

To all it may concern,

Dear BioJava,

My name Omer Frieman and i am a student of Computer Science (B.Sc) and
International Politics at the Hebrew university in Jerusalem, Israel.
Last week, I attended a conference about Google SOC, Which i find most
interesting and something that i would like to experience.
I am in the second year of my degree, and so far i have learned the program
languages: Java, C, C++ and in addition Object Oriented Programming in Java.
Though, i have no working experience in programming.

While searching the list of SOC projects i came across the Bioinformatics
Foundation Projects.
I found the Java Project very interesting, First, for the content - the
research subject of Bio-informatics, and Second, I was looking specifically
for a Java project for gaining experience in it,

Before sending my application with the short coding exercise, i send you
this mail to Introduce myself.
My only concern is,  will My lack of experience could hurt my chances to be
accepted to the project.
I would appreciate  your opinion in that matter.

Furthermore, i was wondering how do i connect the Project mentor (Peter
Troshin).

Sincerely,
 Omer.


From p.v.troshin at dundee.ac.uk  Mon Apr  4 14:33:38 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Mon, 04 Apr 2011 15:33:38 +0100
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>
	<BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>
Message-ID: <4D99D6C2.9060107@dundee.ac.uk>

Hi Omer,

I am on the BioJava list so I got your email.

> >> I am in the second year of my degree, and so far i have learned
> >> the program languages: Java, C, C++ and in addition Object
> >> Oriented Programming in Java.

Sounds good!

> >> Though, i have no working experience in programming.

Thank you for being honest (:-))

> >> My only concern is, will My lack of experience could hurt my
> >> chances to be accepted to the project.

It may but it may not. Some people pick up things pretty quickly - are 
you one of them?
Seriously, have a look at the methods that you are about to implement, 
search the web
for more information about them and see if you have a good idea how to 
do that. You do not have to know anything about the BioJava at this 
stage, you can learn about it later.  For this
project you also need to know the basics of Chemistry and Molecular 
Biology, nothing too
complicated, but still without this knowledge the learning curve for 
this project is going to be pretty steep.

I hope I answered your question.

Regards,
Peter



On 04/04/2011 13:59, omer f wrote:
>  To all it may concern,
>
>  Dear BioJava,
>
>  My name Omer Frieman and i am a student of Computer Science (B.Sc)
>  and International Politics at the Hebrew university in Jerusalem,
>  Israel. Last week, I attended a conference about Google SOC, Which i
>  find most interesting and something that i would like to experience.
>  I am in the second year of my degree, and so far i have learned the
>  program languages: Java, C, C++ and in addition Object Oriented
>  Programming in Java. Though, i have no working experience in
>  programming.
>
>  While searching the list of SOC projects i came across the
>  Bioinformatics Foundation Projects. I found the Java Project very
>  interesting, First, for the content - the research subject of
>  Bio-informatics, and Second, I was looking specifically for a Java
>  project for gaining experience in it,
>
>  Before sending my application with the short coding exercise, i send
>  you this mail to Introduce myself. My only concern is, will My lack
>  of experience could hurt my chances to be accepted to the project. I
>  would appreciate your opinion in that matter.
>
>  Furthermore, i was wondering how do i connect the Project mentor
>  (Peter Troshin).
>
>  Sincerely, Omer. _______________________________________________
>  Biojava-l mailing list - Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l




From x4roth at gmail.com  Mon Apr  4 15:34:13 2011
From: x4roth at gmail.com (Xaroth)
Date: Mon, 4 Apr 2011 11:34:13 -0400
Subject: [Biojava-l] GSoC Intent - Amino Acids Physico-Chemical Properties
	Calculation
Message-ID: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>

Hello everyone and project mentor Peter Troshin,

My name is Justin Pugh. I am a 3rd year Computer Science student at the
University of Central Florida. I am proficient in C and Java and I prefer to
do all of my coding work in Java. I've recently learned about the Google
Summer of Code program and I've been spending the past week or so looking
over the available open-source projects. I am excited about participating in
the GSoC because I have been anxious to be a part of a larger project than
the small-scope programs that I have to write for classes. Sadly, I do not
have any experience doing any programming projects on this scale but I am
very interested in learning. The largest project I have completed was to
write a compiler and virtual machine for PL/0. I'm currently working on
writing a game from scratch as a vehicle for implementing some AI techniques
and I am learning a lot about making use of others' code provided in
libraries and integrating it into my own through the use of jMonkeyEngine
(an open source java-based 3d game engine). I want to take my skills to the
next level with GSoC.

Out of all the projects I have looked at, BioJava has stood out the most for
me (in particular, the Amino Acids Physico-Chemical Properties Calculation
idea). I wanted to work on something written entirely in Java so I wouldnt
have to spend any time learning a new language and I would be able to focus
more on the actual project. I feel like I am able to wrap my head around the
Amino Acids Physico-Chemical Properties Calculation proposal and I think it
falls within my ability to get it done and even more - to have fun with it
and be able to spend time refining it. I do not know anything about the
calculations which must be implemented, but I am of course willing to learn
them. I have only had small instruction in the area of multi-threaded Java
programming but I hope this will not be a severe handicap for me.

I plan on spending the next couple days doing some research and developing
my proposal. I just wanted to announce my intent to submit an application
and to introduce myself to the group. Please let me know your opinions
regarding my ability to complete this project - I am open to criticism and
pointers! :)

Thank you for your time,
-Justin Pugh


From p.v.troshin at dundee.ac.uk  Tue Apr  5 10:23:10 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 11:23:10 +0100
Subject: [Biojava-l] GSoC Intent - Amino Acids Physico-Chemical
 Properties Calculation
In-Reply-To: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
References: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
Message-ID: <4D9AED8E.3070309@dundee.ac.uk>

Hi Justin,

Welcome to the BioJava mailing list and thank you for your interest in 
the project.

It sounds like you have plenty of experience in programming, which is 
definitely a plus. Do not worry about you lack of experience in 
multi-threaded programs, in the end there must be something for you to 
learn too! I hope that this project can give you what you are looking 
for ? the experience of implementing algorithms in pure Java and 
integrating with the relatively large BioJava code base.

However, do not underestimate the difficulty of the algorithms for 
calculating the physico-chemical properties. Although the algorithms may 
not be particularly complex, but in order to understand them you would 
need some knowledge in chemistry, molecular biology and maths. 
Programming skills only will not be sufficient for this project.

Good luck with your application.

Regards,
Peter





On 04/04/2011 16:34, Xaroth wrote:
> Hello everyone and project mentor Peter Troshin,
>
> My name is Justin Pugh. I am a 3rd year Computer Science student at the
> University of Central Florida. I am proficient in C and Java and I prefer to
> do all of my coding work in Java. I've recently learned about the Google
> Summer of Code program and I've been spending the past week or so looking
> over the available open-source projects. I am excited about participating in
> the GSoC because I have been anxious to be a part of a larger project than
> the small-scope programs that I have to write for classes. Sadly, I do not
> have any experience doing any programming projects on this scale but I am
> very interested in learning. The largest project I have completed was to
> write a compiler and virtual machine for PL/0. I'm currently working on
> writing a game from scratch as a vehicle for implementing some AI techniques
> and I am learning a lot about making use of others' code provided in
> libraries and integrating it into my own through the use of jMonkeyEngine
> (an open source java-based 3d game engine). I want to take my skills to the
> next level with GSoC.
>
> Out of all the projects I have looked at, BioJava has stood out the most for
> me (in particular, the Amino Acids Physico-Chemical Properties Calculation
> idea). I wanted to work on something written entirely in Java so I wouldnt
> have to spend any time learning a new language and I would be able to focus
> more on the actual project. I feel like I am able to wrap my head around the
> Amino Acids Physico-Chemical Properties Calculation proposal and I think it
> falls within my ability to get it done and even more - to have fun with it
> and be able to spend time refining it. I do not know anything about the
> calculations which must be implemented, but I am of course willing to learn
> them. I have only had small instruction in the area of multi-threaded Java
> programming but I hope this will not be a severe handicap for me.
>
> I plan on spending the next couple days doing some research and developing
> my proposal. I just wanted to announce my intent to submit an application
> and to introduce myself to the group. Please let me know your opinions
> regarding my ability to complete this project - I am open to criticism and
> pointers! :)
>
> Thank you for your time,
> -Justin Pugh
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From p.v.troshin at dundee.ac.uk  Tue Apr  5 16:00:32 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 17:00:32 +0100
Subject: [Biojava-l] Final Application (Paiu Alexandru ) (added project
 plan)
In-Reply-To: <AANLkTin9Ggi1KMERJ157sxzFbXu9=qFrJi+WRdq0JH=j@mail.gmail.com>
References: <AANLkTin9Ggi1KMERJ157sxzFbXu9=qFrJi+WRdq0JH=j@mail.gmail.com>
Message-ID: <4D9B3CA0.6000707@dundee.ac.uk>

Hi Alex,

I have a look at your plan and I'd suggest that you add a few more 
details into it. Right now I'd say it does not look sufficiently detailed.

What are the deliverables of you project?
What steps you will take at every stage of the project.
How you make sure that your implementation gives the correct results?
Are you going to use BioJava? If so how?

Also, I would not bother with any implementation details as yet.
Finally, If you worked with any version control systems it would help to 
state this.

I hope this will help you to improve your proposal.

Regards,
Peter


On 28/03/2011 17:17, Alexandru Paiu wrote:
> *1.      **1.Your complete contact information*, including full name,
> physical address, preferred email address, and telephone number, plus other
> pertinent contact information such as IRC handles, etc.
>
>
>
> Full Name : Paiu Alexandru
>
> Address : Country Romania , city Constanta , Bld. Aurel Vlaicu , Nr. 41 ,
> Bl. Pc1 sc. B , Et 6 , Apt. 46
>
> E-mail : paiualex12 at google.com or paiualex12 at yahoo.com
>
> Telephone number : 40733924684
>
>
>
> *2.       **2.Why you are interested in the p*roject you are proposing and
> are well-suited to undertake it.
>
>
>
> This project suits me perfectly , because the interested students should
> have a general knowledge of core Java programming, knowledge of
> multi-threaded programming . I?ve started learning Java for 1 and a half
> years , and I used a lot of Threads in applications and projects .
>
> This is the only project that I apply , because I haven?t found a more
> interesting project than this one .
>
>
>
> *3.       **3.A summary of your programming *experience and skills.
>
>
>
> I?ve did a lot of miniproject and applications for school and for me . I?ve
> made projects like :
>
> a)      Lanchat Client-Server using TCP/IP ? I wrote two applications : one
> for the client and one for the server . I used an JApplet for the client
> with Swing elements . I?ve used Threads especially in the server sider
> application , and sockets
>
> b)      Lanchat Peer-to-Peer using UDP and multicasting . I wrote only a
> application for  the client . I used Threads and multicast sockets .
>
> c)       A project for administrating a database , using a JApplet with
> Connector/J and MySql . It has to applications , one for clients and for the
> administrator .
>
>
> *4.        **4.Programs or projects you have previously* authored or
> contributed to  available as open-source, including, if applicable, any past
> Summer of Code involvement.
>
>
>
> I haven?t worked yet for any open-source and a I haven?t any past experience
> with GSoc , and it?s the first time a apply for a open-source project . I
> haven?t either worked for a company .
>
>
>
> *5.       **5. A project plan for the project* you are proposing, even if
> your proposed project is directly based on one of the proposed project ideas
> for member projects.
>
>
>
> I wish to apply to the project called *Amino Acids physic-chemical
> properties calculation .*
>
> I?ve been thinking since some time of a possible implementation and I
> stopped at a single one (that I think it?s the best) .
>
>
>
> I will use two main classes . One that will represent an atom of a substance
> ( for example He , H , O , etc ) , that will have params like : atom weight
> , name , abbreviation , valence .  I?ll use the second class for
> constructing amino-acids from this class . So , the second class will extend
> the class of atoms . So for example I have to initiate a molecule of H20
> (water) . I will have a constructor with a string param , that will build
> the substance . For example , let?s say that the second class it?s called
> Aminoacids , and the first one Atoms .
>
> Let?s say I choose from a Combo box H2O ( it?s only a example) . Then I sad
> the string ? H2O1? to the aminoacids class , to intiate an object of
> aminoacid . That constructor will be evaluated char by char . If it?s found
> a char or two chars that means that I have to initiate an atom of that char
> or chars . If it?s found a number , then that means that it?s the multiplier
> of that atom before it .
>
> So the class aminoacids will have a private Object [] array , in which will
> be number and objects called atoms .
>
> So for H20 the array will look like this : array[0] = atom of H (Hidrogen) ,
> array[1]=2 , array[2]=O (Oxigen) , array[3]=1 .
>
> All the know substances will be in a file called atoms.txt with atom mass ,
> name , abbreviation etc . The atoms class will have a method to add new
> atoms to the list .
>
>
>
> And for calculating the molecular weigth the algorithm is very simple . We
> already have array={H,2,O,1} , and the atoms will have as params the atoms
> weight so all we have to do is just :
>
> Mol. Weight=H.weight*2+O.weigth.*1
>
>
>
> The plan for implementing :
>
>
>
> -          May 20-June 20 ? implementing the two classes and the first two
> methods
>
> -          June 20 ? 20 July ? Implementing the rest of the methods
>
> -          20 July ? until the final ? final retouching , docummentation for
> end users , and 1  method proposed by me
>
> -
>
> *6.       **6.Any obligations, vacations, or plans* for the summer that may
> require scheduling during the GSoC work period.
>
>
>
> I will have School final exams during 20 May ? 20 June . So I won?t be able
> to work at maximum capacity . That?s all . I
>
>
> *7. PS *
>
> I hope you've got my short coding exercise program ( I received a kinda
> error for sending a mail will atachement)
>
> thanks
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From p.v.troshin at dundee.ac.uk  Tue Apr  5 16:44:08 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Tue, 05 Apr 2011 17:44:08 +0100
Subject: [Biojava-l] attention to GSoC Amino Acids Physico-Chemical
 Properties prospective students
In-Reply-To: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
References: <BANLkTinqWioKWxQ_zBoAz=STtH_2=OQE6w@mail.gmail.com>
Message-ID: <4D9B46D8.6070906@dundee.ac.uk>

Hello prospective GSoC students,

A have seen a few project plans so far and none of them seems to go into 
the trouble of providing the formulas for the calculations. Yet, it 
would have definitely strengthened your proposal if you can demonstrate 
that you are capable of extracting this information from the web and/or 
scientific papers. That said you do not have to include everything in 
your proposal but at least show that you know where to find what you 
need. There is the balance here to strike and this is something that is 
going to set you apart.

I'd like to stress that the ideal student for this project should not 
only be a good Java programmer but have a keen interest in 
Bioinformatics! So please feel free to extend the original idea as you 
see fit.

Good luck with your applications,
Peter

P.S.
The project plan is if of cause yours and you should decide whether to 
include anything from the above or leave it, this is only an advice.

Dr Peter Troshin
Bioinformatics Software Developer
Phone: +44 (0)1382 388589
Fax:     +44 (0)1382 385764
The Barton Group
College of Life Sciences
Medical Sciences Institute
University of Dundee
Dundee
DD1 5EH
UK



From andreas at sdsc.edu  Wed Apr  6 04:33:47 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 5 Apr 2011 21:33:47 -0700
Subject: [Biojava-l] last days before submitting for GSoC
Message-ID: <BANLkTim95ye4eNChNyoDdUYbSFcRhOOkPQ@mail.gmail.com>

Hi,

just a quick reminder that the deadline to submit proposals for GSoC
is approaching rapidly (Friday).

In order to correctly apply you need to submit your applications at

http://www.google-melange.com/

Don't forget to discuss your projects with the potential mentors or this list.

A couple of more links that might be useful:

how to write a proposal
http://www.booki.cc/gsocstudentguide/_v/1.0/writing-a-proposal/

Here two proposals that got funded last year:

http://biojava.org/wiki/GSoC:MSA
http://biojava.org/wiki/GSoC:PTM

Andreas


From madhatterkkt at gmail.com  Wed Apr  6 04:37:47 2011
From: madhatterkkt at gmail.com (K T)
Date: Tue, 5 Apr 2011 21:37:47 -0700
Subject: [Biojava-l] Retrieving data from Genbank online
Message-ID: <BANLkTi=qC4-kkqjvYTf4BZanTZLUuTnkUg@mail.gmail.com>

I'm new to BioJava3, and recently downloaded 3.0.1.  I'm looking for a way
to retrieve entries from NCBI online (not a flat-file) using a RefSeq
accession ID.  I was able to do this with BioPerl, and I've also seen that
there was a way to do this under BioJava 1.x.  Can someone point me to a
code-snippet where this is done for BioJava3?

I tried searching online, but most of my search hits point either to BioJava
1.x or refer to retrieving them from a flat-file.  I'm trying to get it from
NCBI's online database directly.

Thanks in advance.


From alastair.m.kilpatrick at googlemail.com  Wed Apr  6 09:07:27 2011
From: alastair.m.kilpatrick at googlemail.com (Alastair Kilpatrick)
Date: Wed, 6 Apr 2011 10:07:27 +0100
Subject: [Biojava-l] Multiple sequence alignment in BioJava
Message-ID: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>

Dear all,
I'm pretty new to BioJava so I may be missing something - I've checked
through the list archives without much luck.
I've been trying to do some multiple sequence alignments but I've been
running into strange errors. To try and find where the problem is,
I've just copied the code straight from
http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
I'm still getting an error:

Caused by: java.lang.ClassNotFoundException:
org.forester.phylogenyinference.DistanceMatrix

It would seem that this is something to do with forester.jar, which I
had to download separately (from http://code.google.com/p/forester/)
as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
when I look through the jar in Eclipse, there isn't anything named
'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
'phylogeny.factories' and 'phylogeny.iterators'. Is there something
I'm doing wrong, or is it the case that either one of BioJava or
forester has been updated and things have broken somewhere (I see the
CookBook page was updated in July 2010 but forester was updated just
last month)? Either way, any ideas would be much appreciated!

Many thanks,
Alastair Kilpatrick

PhD candidate,
School of Informatics, University of Edinburgh


From alastair.m.kilpatrick at googlemail.com  Wed Apr  6 16:40:26 2011
From: alastair.m.kilpatrick at googlemail.com (Alastair Kilpatrick)
Date: Wed, 6 Apr 2011 17:40:26 +0100
Subject: [Biojava-l] Multiple sequence alignment in BioJava
In-Reply-To: <BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
References: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>
	<BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
Message-ID: <BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>

Thanks - I had just downloaded the BioJava jars manually so that's
fixed the CookBook code. However, I've made some changes in order to
align DNA sequences instead and am running into more errors - this
code:

	public static void main(String[] args) {
		String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"};
		List<DNASequence> lst = new ArrayList<DNASequence>();
		for(String seq : seqs) {
			lst.add(new DNASequence(seq));
		}
		Profile<DNASequence, NucleotideCompound> profile =
Alignments.getMultipleSequenceAlignment(lst); //**
		System.out.println(profile);
		ConcurrencyTools.shutdown();
	}

gives:
java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
	at java.util.concurrent.FutureTask.get(Unknown Source)
	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
	at CookbookMSA.main(CookbookMSA.java:49)

at the 'alignment' line (**) - not sure what the problem is here, I
see that getMultipleSequenceAlignment() has an extra argument(s) in
the Javadoc but these weren't required in the example?
Final question (hopefully!) - once I have the alignments I require I'd
like to create a sequence logo - is there a way of doing this in
BioJava3? From a google search I've seen references to
DistributionTools.distOverAlignment() and similar, but can't find
anything like that in the new api.

Thanks again, sorry everyone for all the questions!

Alastair


On 6 April 2011 12:09, Scooter Willis <willishf at gmail.com> wrote:
>
> You need to use the forester.jar file from the biojava3 code check out. If you are using maven this should be automatic.
>
> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" <alastair.m.kilpatrick at googlemail.com> wrote:
>
> Dear all,
> I'm pretty new to BioJava so I may be missing something - I've checked
> through the list archives without much luck.
> I've been trying to do some multiple sequence alignments but I've been
> running into strange errors. To try and find where the problem is,
> I've just copied the code straight from
> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
> I'm still getting an error:
>
> Caused by: java.lang.ClassNotFoundException:
> org.forester.phylogenyinference.DistanceMatrix
>
> It would seem that this is something to do with forester.jar, which I
> had to download separately (from http://code.google.com/p/forester/)
> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
> when I look through the jar in Eclipse, there isn't anything named
> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something
> I'm doing wrong, or is it the case that either one of BioJava or
> forester has been updated and things have broken somewhere (I see the
> CookBook page was updated in July 2010 but forester was updated just
> last month)? Either way, any ideas would be much appreciated!
>
> Many thanks,
> Alastair Kilpatrick
>
> PhD candidate,
> School of Informatics, University of Edinburgh
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From paiualex12 at gmail.com  Wed Apr  6 17:05:38 2011
From: paiualex12 at gmail.com (Alexandru Paiu)
Date: Wed, 6 Apr 2011 20:05:38 +0300
Subject: [Biojava-l] Identified bug in BioJava(Paiu Alexandru)
Message-ID: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>

Hi to all .
I've identified a bug in BioJava .
Usually the first element in an array is on index 0 (pos 0 ) .
I've tried to learn more about Java and I've tryed the next 2 instructions :

ProteinSequence a=new ProteinSequence("A");
AminoAcidCompound b=a.getCompoundAt(0);


This will give a null execption (out of array bounds or something like that
) .
when I put AminoAcidCompound b=a.getCompoundAt(1);  it works and identifies
the first
aminoacid as Alanine .

That's all for today


From willishf at ufl.edu  Wed Apr  6 18:30:11 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Wed, 6 Apr 2011 14:30:11 -0400
Subject: [Biojava-l] Identified bug in BioJava(Paiu Alexandru)
In-Reply-To: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>
References: <BANLkTinznBG=X+kBYXn7TQ=g7N9jCJGyJw@mail.gmail.com>
Message-ID: <BANLkTi=hf1ygb0_xq=_rzcFjY+QAMbJyTw@mail.gmail.com>

Alexandru

To make it easier on how biologist think about the first position(1)
versus how computer scientists think(0) we opted to go with the
biologist view of the world. So use 1 for the first sequence position.

Thanks

Scooter

On Wed, Apr 6, 2011 at 1:05 PM, Alexandru Paiu <paiualex12 at gmail.com> wrote:
> Hi to all .
> I've identified a bug in BioJava .
> Usually the first element in an array is on index 0 (pos 0 ) .
> I've tried to learn more about Java and I've tryed the next 2 instructions :
>
> ProteinSequence a=new ProteinSequence("A");
> AminoAcidCompound b=a.getCompoundAt(0);
>
>
> This will give a null execption (out of array bounds or something like that
> ) .
> when I put AminoAcidCompound b=a.getCompoundAt(1); ?it works and identifies
> the first
> aminoacid as Alanine .
>
> That's all for today
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>



From andreas at sdsc.edu  Thu Apr  7 05:03:40 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 6 Apr 2011 22:03:40 -0700
Subject: [Biojava-l] Multiple sequence alignment in BioJava
In-Reply-To: <BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>
References: <BANLkTi=i9Ksr+3mu4uPtMwYx7nQ_pJcu_Q@mail.gmail.com>
	<BANLkTinHPP83WraWNLHxREGiTEyWhfwoMg@mail.gmail.com>
	<BANLkTiky_NYVSxit51EukUYpZ2wmBUmLFQ@mail.gmail.com>
Message-ID: <BANLkTi==xE9cSfejyuDO_84WmrtdE6JHDA@mail.gmail.com>

Hi Alastair,

BioJava 1.X can do distributions, however there is no counterpart for
this yet in BioJava 3.

Andreas

On Wed, Apr 6, 2011 at 9:40 AM, Alastair Kilpatrick
<alastair.m.kilpatrick at googlemail.com> wrote:
> Thanks - I had just downloaded the BioJava jars manually so that's
> fixed the CookBook code. However, I've made some changes in order to
> align DNA sequences instead and am running into more errors - this
> code:
>
> ? ? ? ?public static void main(String[] args) {
> ? ? ? ? ? ? ? ?String[] seqs = {"GATTACATTT", "CGATTACATG", "ATGGATTACA"};
> ? ? ? ? ? ? ? ?List<DNASequence> lst = new ArrayList<DNASequence>();
> ? ? ? ? ? ? ? ?for(String seq : seqs) {
> ? ? ? ? ? ? ? ? ? ? ? ?lst.add(new DNASequence(seq));
> ? ? ? ? ? ? ? ?}
> ? ? ? ? ? ? ? ?Profile<DNASequence, NucleotideCompound> profile =
> Alignments.getMultipleSequenceAlignment(lst); //**
> ? ? ? ? ? ? ? ?System.out.println(profile);
> ? ? ? ? ? ? ? ?ConcurrencyTools.shutdown();
> ? ? ? ?}
>
> gives:
> java.util.concurrent.ExecutionException: java.lang.NullPointerException
> ? ? ? ?at java.util.concurrent.FutureTask$Sync.innerGet(Unknown Source)
> ? ? ? ?at java.util.concurrent.FutureTask.get(Unknown Source)
> ? ? ? ?at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)
> ? ? ? ?at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)
> ? ? ? ?at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)
> ? ? ? ?at CookbookMSA.main(CookbookMSA.java:49)
>
> at the 'alignment' line (**) - not sure what the problem is here, I
> see that getMultipleSequenceAlignment() has an extra argument(s) in
> the Javadoc but these weren't required in the example?
> Final question (hopefully!) - once I have the alignments I require I'd
> like to create a sequence logo - is there a way of doing this in
> BioJava3? From a google search I've seen references to
> DistributionTools.distOverAlignment() and similar, but can't find
> anything like that in the new api.
>
> Thanks again, sorry everyone for all the questions!
>
> Alastair
>
>
> On 6 April 2011 12:09, Scooter Willis <willishf at gmail.com> wrote:
>>
>> You need to use the forester.jar file from the biojava3 code check out. If you are using maven this should be automatic.
>>
>> On Apr 6, 2011 5:07 AM, "Alastair Kilpatrick" <alastair.m.kilpatrick at googlemail.com> wrote:
>>
>> Dear all,
>> I'm pretty new to BioJava so I may be missing something - I've checked
>> through the list archives without much luck.
>> I've been trying to do some multiple sequence alignments but I've been
>> running into strange errors. To try and find where the problem is,
>> I've just copied the code straight from
>> http://biojava.org/wiki/BioJava:CookBook3:MSA and tried to run it, but
>> I'm still getting an error:
>>
>> Caused by: java.lang.ClassNotFoundException:
>> org.forester.phylogenyinference.DistanceMatrix
>>
>> It would seem that this is something to do with forester.jar, which I
>> had to download separately (from http://code.google.com/p/forester/)
>> as per http://biojava.org/wiki/BioJava:CookBook#biojava3-alignment -
>> when I look through the jar in Eclipse, there isn't anything named
>> 'phylogenyinference', although there is 'phylogeny', 'phylogeny.data',
>> 'phylogeny.factories' and 'phylogeny.iterators'. Is there something
>> I'm doing wrong, or is it the case that either one of BioJava or
>> forester has been updated and things have broken somewhere (I see the
>> CookBook page was updated in July 2010 but forester was updated just
>> last month)? Either way, any ideas would be much appreciated!
>>
>> Many thanks,
>> Alastair Kilpatrick
>>
>> PhD candidate,
>> School of Informatics, University of Edinburgh
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From effat34 at gmail.com  Thu Apr  7 11:26:43 2011
From: effat34 at gmail.com (effat farhana)
Date: Thu, 7 Apr 2011 17:26:43 +0600
Subject: [Biojava-l] Amino acids physico-chemical properties calculation
Message-ID: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>

Hi,
I'm a student of Computer Science and Engineering background. I heard about
GSoC a few days earlier and very much eager to participate in it. I'm quite
familiar with C++, Java multithreading. The idea of this project proposal
seems quite interesting to me.

One of the methods to be implemented is to calculate the numbers of
different amino  acids in protein.
Would you please explain how the input of this method will be given? Will
the protein sequence be represented by String as sequence of amino acids and
I've just count the different types of amino acid?


Looking forward for your quick reply
Thanks in advance

farhana


From p.v.troshin at dundee.ac.uk  Thu Apr  7 21:47:20 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 07 Apr 2011 22:47:20 +0100
Subject: [Biojava-l] Amino acids physico-chemical properties calculation
In-Reply-To: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>
References: <BANLkTik9L6-_wM0bK4LxBFtWFjXLG3UUuA@mail.gmail.com>
Message-ID: <4D9E30E8.3090501@dundee.ac.uk>

> >> Would you please explain how the input of this method will be
> >> given?

Just assume that this would be a String for now. For example 
"MFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR".

Hope that helps.

Regards,
Peter

On 07/04/2011 12:26, effat farhana wrote:
>  Hi, I'm a student of Computer Science and Engineering background. I
>  heard about GSoC a few days earlier and very much eager to
>  participate in it. I'm quite familiar with C++, Java multithreading.
>  The idea of this project proposal seems quite interesting to me.
>
>  One of the methods to be implemented is to calculate the numbers of
>  different amino acids in protein. Would you please explain how the
>  input of this method will be given? Will the protein sequence be
>  represented by String as sequence of amino acids and I've just count
>  the different types of amino acid?
>
>
>  Looking forward for your quick reply Thanks in advance
>
>  farhana _______________________________________________ Biojava-l
>  mailing list - Biojava-l at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-l




From p.v.troshin at dundee.ac.uk  Thu Apr  7 22:26:39 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Thu, 07 Apr 2011 23:26:39 +0100
Subject: [Biojava-l] google summer of code proposal
In-Reply-To: <BANLkTi=4Ds3mMHepozgfjAe2W2Guj7GgJQ@mail.gmail.com>
References: <BANLkTi=4Ds3mMHepozgfjAe2W2Guj7GgJQ@mail.gmail.com>
Message-ID: <4D9E3A1F.8050306@dundee.ac.uk>

Dear Mihaly,

I am sorry for belated response. I'd suggest simplifying your plan a 
little. For example you do not need to write what you are going to do 
every day of GSoC. One week precision will be fine. On the other hand, 
it would be good to include formulas into the plan as well as expand the 
original idea with something that is in line with the project and 
interest you.

Did you have a go at the coding exercise? If not I would recommend you 
to do that.
Finally do not forget to send your proposal to melange.

Regards,
Peter


On 06/04/2011 21:35, Mihaly Cs?k?s wrote:
>
> Dear Peter,
>
> I am very interested in gsoc and I would like to apply for the BioJava 
> - Amino acids physico-chemical properties calculation project.
>
> I send you my Proposal in the attachment. Please if you have a little 
> time, read it throughand write me your opinion.
>
> Thank you in advance!
>
> Yours sincerely:
>
> Mihaly Csokas
>



From andreas at sdsc.edu  Fri Apr  8 04:45:41 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 7 Apr 2011 21:45:41 -0700
Subject: [Biojava-l] GSoC last day to submit proposals
Message-ID: <BANLkTikBWp4exPDaVnKAE6BeJ6kcyOiJiw@mail.gmail.com>

Hi,

This is the final reminder that the deadline for submitting proposals
for the Google Summer of Code is Friday April 8th, 19:00 UTC.

Andreas


From kohchuanhock at gmail.com  Fri Apr  8 17:46:21 2011
From: kohchuanhock at gmail.com (Chuan Hock Koh)
Date: Sat, 9 Apr 2011 01:46:21 +0800
Subject: [Biojava-l] Submission of Short Coding Exercise
Message-ID: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>

Dear Dr Peter Troshin,

I had completed the short coding exercise. As I was about to submit it, I
realize that I am unsure about the behavior that runme.jar should exhibit.

In Goal 2, it was given that the example command is "java FindEnds
inputFile.txt outputFile.txt"

Am I right to say that runme.jar should replace FindEnds and run as follows?

"java -jar runme.jar inputFile.txt outputFile.txt"

Please advice. Thanks.

Looking forward to your reply.

Regards,
Chuan Hock

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>


From p.v.troshin at dundee.ac.uk  Fri Apr  8 21:43:29 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Fri, 08 Apr 2011 22:43:29 +0100
Subject: [Biojava-l] Submission of Short Coding Exercise
In-Reply-To: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>
References: <BANLkTikeCCZV0gs3qWG7OrKQLLbJZrPwrw@mail.gmail.com>
Message-ID: <4D9F8181.9040204@dundee.ac.uk>

Hello Chuan,

Yes, you are right.

Peter

On 08/04/2011 18:46, Chuan Hock Koh wrote:
> Dear Dr Peter Troshin,
>
> I had completed the short coding exercise. As I was about to submit it, I
> realize that I am unsure about the behavior that runme.jar should exhibit.
>
> In Goal 2, it was given that the example command is "java FindEnds
> inputFile.txt outputFile.txt"
>
> Am I right to say that runme.jar should replace FindEnds and run as follows?
>
> "java -jar runme.jar inputFile.txt outputFile.txt"
>
> Please advice. Thanks.
>
> Looking forward to your reply.t.
>
> Regards,
> Chuan Hock
>



From khalil.elmazouari at gmail.com  Mon Apr 11 20:25:15 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Mon, 11 Apr 2011 22:25:15 +0200
Subject: [Biojava-l] RichSequenceIterator.hasNext from empty file return
	true!!!
Message-ID: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>

Hi,

RichSequenceIterator.hasNext from empty file return true!!! and throws an infinite BioException loop!!!
Any explanation?? Thanks

khalil

test using the following code

    public static void main(String[] args) {
       String path = "emptyFile.txt";

         BufferedReader br = null;
      try {
         br = new BufferedReader(new FileReader(path));
      } catch (FileNotFoundException ex) {
         ex.printStackTrace();
      }
      RichSequenceIterator seqs = RichSequence.IOTools.readFastaProtein(br, null);
        while (seqs.hasNext()) {
         try {
            RichSequence seq = seqs.nextRichSequence();
         } catch (NoSuchElementException ex) {
            ex.printStackTrace();
         } catch (BioException ex) {
            ex.printStackTrace();
         }
        }

====

org.biojava.bio.BioException: Could not read sequence
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at com.kem.ae.core.Empty.main(Empty.java:51)
Caused by: java.io.IOException: Premature stream end
        at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
        ... 1 more
org.biojava.bio.BioException: Could not read sequence
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
        at com.kem.ae.core.Empty.main(Empty.java:51)
Caused by: java.io.IOException: Premature stream end
        at org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
        at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)

infinite loop....




From chapmanb at 50mail.com  Tue Apr 12 12:36:32 2011
From: chapmanb at 50mail.com (Brad Chapman)
Date: Tue, 12 Apr 2011 08:36:32 -0400
Subject: [Biojava-l] Bioinformatics Open Source Conference (BOSC
 2011)--Abstracts due April 18th!
Message-ID: <20110412123632.GE2105@kunkel>

Only one week left to submit an abstract to BOSC 2011! We have
two great keynote speakers lined up (Lawrence Hunter and Matt
Wood) and session topics that include parallel and cloud-based
approaches to bioinformatics, genome content management, and tools for
next-generation sequencing. We'd love to hear about your Open Source
bioinformatics project!

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011)
An ISMB 2011 Special Interest Group (SIG)
July 15-16, 2011, in Vienna, Austria
http://www.open-bio.org/wiki/BOSC_2011

Important Dates:
April 18, 2011: Deadline for submitting abstracts to BOSC 2011
May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors
July 13-14, 2011: Codefest 2011 programming session 
  (see http://www.open-bio.org/wiki/Codefest_2011 for details)
July 15-16, 2011: BOSC 2011
July 17-19, 2011: ISMB 2011

The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.

We invite you to submit abstracts for talks and posters.  Sessions include:
- Approaches to parallel processing
- Cloud-based approaches to improving software and data accessibility
- The Semantic Web in open source bioinformatics
- Data visualization
- Tools for next-generation sequencing
- Other Open Source software

In addition to the above sessions, there will be a panel discussion
about "Meeting the challenges of inter-institutional collaboration".
We are also working to arrange a joint session with one of the other
ISMB SIGs.

Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards for BOSC 2011. Each winner will be awarded $250 to
defray the costs of travel to BOSC 2011. All students whose abstracts
are accepted for talks will be considered for this award.

For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information

BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice
(co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London,
Ron Taylor


From gwaldon at geneinfinity.org  Tue Apr 12 18:02:28 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 12 Apr 2011 13:02:28 -0500
Subject: [Biojava-l] RichSequenceIterator.hasNext from empty file return
 true!!!
In-Reply-To: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>
References: <63EB0592-5431-4AB1-A73A-744832E7B547@gmail.com>
Message-ID: <20110412130228.31866c2hd15fztm8@gator1273.hostgator.com>

Hi Khali,

In my hands I found "java.io.FileNotFoundException: emptyFile.txt (The  
system cannot find the file specified)", which is not exactly the same  
thing as an empty file. Anyway, I think you are right and  
RichStreamReader should switch the moreSequenceAvailable flag before  
throwing the exception. In your case just get out of the loop and you  
should be safe. Thanks for reporting.

George

Quoting Khalil El Mazouari <khalil.elmazouari at gmail.com>:

> Hi,
>
> RichSequenceIterator.hasNext from empty file return true!!! and  
> throws an infinite BioException loop!!!
> Any explanation?? Thanks
>
> khalil
>
> test using the following code
>
>     public static void main(String[] args) {
>        String path = "emptyFile.txt";
>
>          BufferedReader br = null;
>       try {
>          br = new BufferedReader(new FileReader(path));
>       } catch (FileNotFoundException ex) {
>          ex.printStackTrace();
>       }
>       RichSequenceIterator seqs =  
> RichSequence.IOTools.readFastaProtein(br, null);
>         while (seqs.hasNext()) {
>          try {
>             RichSequence seq = seqs.nextRichSequence();
>          } catch (NoSuchElementException ex) {
>             ex.printStackTrace();
>          } catch (BioException ex) {
>             ex.printStackTrace();
>          }
>         }
>
> ====
>
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>         ... 1 more
> org.biojava.bio.BioException: Could not read sequence
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)
>         at com.kem.ae.core.Empty.main(Empty.java:51)
> Caused by: java.io.IOException: Premature stream end
>         at  
> org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:178)
>         at  
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>
> infinite loop....
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>





From mandarijnopw8 at gmail.com  Wed Apr 13 14:47:12 2011
From: mandarijnopw8 at gmail.com (Shamanou van Leeuwen)
Date: Wed, 13 Apr 2011 16:47:12 +0200
Subject: [Biojava-l] GSOC
Message-ID: <4DA5B770.7040809@gmail.com>

Hi everyone,

i am student who would like to join GSOC with another programmer.
But we still are in need of a mentor who can guide us.

is there someone with biojava experience who can help us during GSOC?

greetings,
Shamanou van Leeuwen




From rmb32 at cornell.edu  Wed Apr 13 15:30:59 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 13 Apr 2011 08:30:59 -0700
Subject: [Biojava-l] last call for Google Summer of Code mentors
Message-ID: <4DA5C1B3.4010504@cornell.edu>

Hi all,

This is the last call for mentors for Google Summer of Code.  We have a 
good crop of student proposals this year for doing work on OBF projects, 
and money from Google to fund them, but we need experienced Bio* 
developers to mentor them.

If you'd like to see the student proposals, participate in their 
scoring, and possibly volunteer to mentor them (remotely of course) over 
the summer, do two things:

1.) Create an account on http://google-melange.com and send a request to 
be an admin from the OBF page on there, 
http://www.google-melange.com/gsoc/org/google/gsoc2011/obf

2.) Join the OBF GSoC mentors mailing list at
http://lists.open-bio.org/mailman/listinfo/gsoc-mentors

Even if you just want to see the student applications and help with 
scoring, but don't necessarily have time to mentor a student, your input 
in the scoring process is appreciated.  :-)

Rob

----
Robert Buels
OBF GSoC 2011 Administrator




From andreas at sdsc.edu  Thu Apr 14 03:17:29 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 13 Apr 2011 20:17:29 -0700
Subject: [Biojava-l] GSOC
In-Reply-To: <4DA5B770.7040809@gmail.com>
References: <4DA5B770.7040809@gmail.com>
Message-ID: <BANLkTi=AANj4tXqHegPF=SrVzqv9z0Wn+g@mail.gmail.com>

Hi Shamanou,

The deadline for submitting proposals was last Friday. Usually the
funding is for one student only and not for pairs of students...

Andreas

On Wed, Apr 13, 2011 at 7:47 AM, Shamanou van Leeuwen
<mandarijnopw8 at gmail.com> wrote:
> Hi everyone,
>
> i am student who would like to join GSOC with another programmer.
> But we still are in need of a mentor who can guide us.
>
> is there someone with biojava experience who can help us during GSOC?
>
> greetings,
> Shamanou van Leeuwen
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From p.v.troshin at dundee.ac.uk  Wed Apr  6 15:49:59 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 06 Apr 2011 16:49:59 +0100
Subject: [Biojava-l] Fwd: Google Summer of Coding: Java project
In-Reply-To: <BANLkTinfMi-XDkqnnxrVnMqfjaLttHuEKQ@mail.gmail.com>
References: <BANLkTinS1U6Pj+2xMSi_AToUkX65YETy0g@mail.gmail.com>	<BANLkTin9LJm_sgg82ZET35G=pKPPwHzwgg@mail.gmail.com>	<4D99D6C2.9060107@dundee.ac.uk>
	<BANLkTinfMi-XDkqnnxrVnMqfjaLttHuEKQ@mail.gmail.com>
Message-ID: <4D9C8BA7.4020806@dundee.ac.uk>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110406/f1be172e/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: molecularweight.gif
Type: image/gif
Size: 1390 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20110406/f1be172e/attachment-0002.gif>

From mostafa.shokrof at gmail.com  Thu Apr 14 11:35:57 2011
From: mostafa.shokrof at gmail.com (Mostafa Shokrof)
Date: Thu, 14 Apr 2011 13:35:57 +0200
Subject: [Biojava-l] Google summer code proposal
Message-ID: <BANLkTi=_tN87ukG9=LNgg5=+XdA94E+nSQ@mail.gmail.com>

On Thu, Apr 14, 2011 at 8:48 AM, Jason Stajich <jason.stajich at gmail.com>wrote:

> Mostafa -
>
> I may have accidently deleted your post to biojava-l about GSOC that was in
> the held queue for the mailiman system. If you can resend it to the list one
> more time I will make sure it goes through.
>
>
> Name :Mostafa EL-Sayed Shokrof
>
> Email:mostafa.shokrof at gmail.com
>
> Physical Address:7 el gomhoreya off tarh el bahr st - el shark -portsaid
> -Egypt
>
> Telephone Number:02-016755576
>
> I am a third year student in Bioinformatics department computer science
> faculty Ain shams university with average grade A. I am interested in
> applying for amino acid properties calculation project which-i do believe-
> is a great opportunity to enhance my experience. I chose Open-Bio
> organization as it offers interaction with real world Bioinformatics applications
> which would certainly help me a lot in my graduation project next semester.
> Choosing this project in particular was based on several reasons. Firstly I
> believe in the project's importance as it addresses core Bioinformatics
> problems and applies Bioinformatics algorithms..Second it will be
> implemented in Java ,which has two main advantages ,it is Object oriented
> and cross platform . ,so I think BIO-Java project is very useful.
>
> I also believe I am well suited for this project as I passed both
> Algorithms and OOP courses with grade A ,besides my strong background in
> biology as I studied biology and Bioinformatics at college.
>
> Not only did I gain my programming experience by attending training courses
> in CIT Global Mobi dev company for mobile applications last summer , but I
> also studied the following courses:
>
> 1.Structural Programming
>
> 2.Data Structure
>
> 3.OOP
>
> 4.Algorithms
>
> 5.File Organization
>
> 6.Software Engineering
>
> Courses being studied this semester are:
>
> 6.Numerical Analysis
>
> 7.System Analysis
>
>
>
> Concerning my biological background,I have studied:
>
> 1.Introduction to Biology
>
> 2.Introduction to Biochemistry
>
> 3.Introduction to Biophysics
>
> 4.Introduction to Molecular Cell Biology
>
> 5.Advanced Molecular Genetics
>
> 6.Introduction to Bioinformatics
>
> Courses being studied in this semester:
>
> 7.Biotechnology
>
> 8.Structural Bioinformatics
>
>
>
> Unfortunately Google schedule does not fit me since our exams are expected
> to be delayed due to the current circumstances in Egypt ,so I hope I will be
> free on the beginning of July .
>
> But after that I will dedicate my summer to GSCO .I can work an average 8
> hours a day ,five days a week of total 40 hours a week. The New semester
> starts at the half of September. so I will have plenty of time .Finally I
> would be really grateful if you provided me this cherish opportunity which
> would help me out in my career further on.
>
>
>
>
>
> I attached time line for the project ,UML design ,Abstract of how the
> implementation will look and , the Short code Exercise with the proposal,
>
> I will appreciate your feedback..
>
resourceshttps://
> docs.google.com/leaf?id=0B-lMAeKAGH9gYjFjNWFmZmItMGZkMC00NDIwLWFlODgtMDUzYzhlYWEwNzk0&hl=en:
>
>
> my regards,
>
> Mostafa Shokrof
>
> Bioinformatics student
> Ain Shams University
>


From erikclarke at gmail.com  Fri Apr 15 02:41:48 2011
From: erikclarke at gmail.com (Erik C)
Date: Thu, 14 Apr 2011 19:41:48 -0700
Subject: [Biojava-l] needleman-wunsch score problems
Message-ID: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>

Hi all,
I'm having some trouble reconciling the scores from the NeedlemanWunsch
sequence alignment object in BioJava with the scores I'm getting from the
EMBL-EBI command-line tool 'needle'. Specifically, for the same sequences,
matrix, and penalties, BioJava returns 274 (in one case), while `needle'
returns 163.
Does anybody have any ideas as to why this might be happening? Is there a
parameter or setting I'm missing? My implementation of the n.w. code in
biojava is below:

    public long alignTwoSequences(ProteinSequence subject,
            ProteinSequence target) {

        SubstitutionMatrix<AminoAcidCompound> blosum62 =
SubstitutionMatrixHelper.getBlosum62();
        GapPenalty penalties = new SimpleGapPenalty();
        penalties.setExtensionPenalty((short) .5);
        penalties.setOpenPenalty((short) 10);
        NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new
NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(subject, target,
penalties, blosum62);
        return nw.getScore();

    }

Thanks,
Erik


From andreas at sdsc.edu  Fri Apr 15 03:14:16 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 14 Apr 2011 20:14:16 -0700
Subject: [Biojava-l] needleman-wunsch score problems
In-Reply-To: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>
References: <BANLkTimJiJbCh_Cjo1ufFmraxKPHvzRo6Q@mail.gmail.com>
Message-ID: <BANLkTimBKs0XZkfie9Jd-rGtZVkN+-DPkg@mail.gmail.com>

Hi Eric,

Did you compare the alignments, i.e which pairs of amino acids are
getting aligned? There might be subtle differences..

Andreas


On Thu, Apr 14, 2011 at 7:41 PM, Erik C <erikclarke at gmail.com> wrote:
> Hi all,
> I'm having some trouble reconciling the scores from the NeedlemanWunsch
> sequence alignment object in BioJava with the scores I'm getting from the
> EMBL-EBI command-line tool 'needle'. Specifically, for the same sequences,
> matrix, and penalties, BioJava returns 274 (in one case), while `needle'
> returns 163.
> Does anybody have any ideas as to why this might be happening? Is there a
> parameter or setting I'm missing? My implementation of the n.w. code in
> biojava is below:
>
> ? ?public long alignTwoSequences(ProteinSequence subject,
> ? ? ? ? ? ?ProteinSequence target) {
>
> ? ? ? ?SubstitutionMatrix<AminoAcidCompound> blosum62 =
> SubstitutionMatrixHelper.getBlosum62();
> ? ? ? ?GapPenalty penalties = new SimpleGapPenalty();
> ? ? ? ?penalties.setExtensionPenalty((short) .5);
> ? ? ? ?penalties.setOpenPenalty((short) 10);
> ? ? ? ?NeedlemanWunsch<ProteinSequence, AminoAcidCompound> nw = new
> NeedlemanWunsch<ProteinSequence, AminoAcidCompound>(subject, target,
> penalties, blosum62);
> ? ? ? ?return nw.getScore();
>
> ? ?}
>
> Thanks,
> Erik
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jayunit100 at gmail.com  Fri Apr 15 17:16:18 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Fri, 15 Apr 2011 13:16:18 -0400
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
Message-ID: <BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>

I adopted a java Needlman Wunsch for proteins and it works fine ; if someone
wants to integrate it or integrate or compare it w/ biojava's implementation
i can provide it just email me i will send the source .

otherwise i can potentially just try to commit it to a sandbox repo if one
exists....


From andreas at sdsc.edu  Fri Apr 15 19:14:34 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 15 Apr 2011 12:14:34 -0700
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
Message-ID: <BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>

Hi Jay,

CCing the list again, somehow I dropped it off this thread.. If I
understand your example right, you want the alignment to only span the
domain that is share between the two proteins. This suggests you would
use a local alignment, not penalizing end gaps.. If you provide some
example IDs we can be more specific...

Andreas



On Fri, Apr 15, 2011 at 11:32 AM, JAX <jayunit100 at gmail.com> wrote:
> Thanks andreas : ?Is there a way to globally align to sequences using smith watermans optimal local alignment; I.e. So as to get an ideal alignment of two multi domain proteins (which only share one domain), that is gapped in such a way so as to cover the whole protein length?
>
> Sent from my iPad
>
> Sent from my iPad
>
> On Apr 15, 2011, at 2:00 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi Jay,
>>
>> thanks for the suggestion. There is already a needleman wunsch and
>> smith waterman implementation available as part of the alignment
>> module. Have you seen those?
>>
>> http://biojava.org/wiki/BioJava:CookBook3:PSA
>>
>> Andreas
>>
>> On Fri, Apr 15, 2011 at 10:16 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
>>> I adopted a java Needlman Wunsch for proteins and it works fine ; if someone
>>> wants to integrate it or integrate or compare it w/ biojava's implementation
>>> i can provide it just email me i will send the source .
>>>
>>> otherwise i can potentially just try to commit it to a sandbox repo if one
>>> exists....
>>> _______________________________________________
>>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>



From jayunit100 at gmail.com  Fri Apr 15 19:30:30 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Fri, 15 Apr 2011 15:30:30 -0400
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
	<BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
Message-ID: <BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>

Consider Kalirin , a multidomain protein.

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=NP_003938.1

Now, lets say I aligned Kalirin with a single domain member of the RHO-Gef
family....  Then only one part of the sequence would match....  But what if
I WANTED a global alignment, for programmatic purposes... Then I would want
an alignment like this

------------------------------------------------RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF------

With lots of gaps in the beggining, and lots of matches at the end, where
the length of the alignment between the two proteins was exactly equivalent.
 Contrast this with a smith waterman output, which would look like this :

RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF....

So is there a way to get the specificity of Smith Waterman in a Needlman
Wunsch alignment ?


From andreas at sdsc.edu  Fri Apr 15 21:49:36 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 15 Apr 2011 14:49:36 -0700
Subject: [Biojava-l] Biojava-l Digest, Vol 99, Issue 12
In-Reply-To: <BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>
References: <mailman.5.1302883209.25213.biojava-l@lists.open-bio.org>
	<BANLkTik_6sdjdQ-mtjtjbWXyO8sbqTL4mg@mail.gmail.com>
	<BANLkTi=1cbrmXE=GUyOGCuXWAD00OAj3Dw@mail.gmail.com>
	<507BA137-A032-4D2E-AAF6-10898EB411B6@gmail.com>
	<BANLkTin0SiGAdhYhic8DYNZro-Q3bUV+mg@mail.gmail.com>
	<BANLkTikDtKFz71nM926EHkg0MHGxbp8ByQ@mail.gmail.com>
Message-ID: <BANLkTimF+P-88=WGeCuOZR1paBF5ko2YTg@mail.gmail.com>

It sounds like you are talking about doing a needleman wunsch
alignment, while not penalizing end gaps. This should give you quite
similar results to just doing a
smith waterman one.

Is it the alignment display that you are concerned about? You could
easily fill up the ends with unaligned regions for smith waterman
results.  I don't find end-gaps particularly informative. Usually an
alignment display will give you the aligned positions, then you can
easily see (or script) if there are end gaps.

Hope that makes sense..
Andreas



On Fri, Apr 15, 2011 at 12:30 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Consider Kalirin , a multidomain protein.
> http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?INPUT_TYPE=live&SEQUENCE=NP_003938.1
> Now, lets say I aligned Kalirin with a single domain member of the RHO-Gef
> family.... ?Then only one part of the sequence would match.... ?But what if
> I WANTED a global alignment, for programmatic purposes... Then I would want
> an alignment like this
> ------------------------------------------------RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF------
> With lots of gaps in the beggining, and lots of matches at the end, where
> the length of the alignment between the two proteins was exactly equivalent.
> ?Contrast this with a smith waterman output, which would look like this :
> RHOGEFRHOGEFRHOG--FRHOGEFRHOGEFRHOGEF....
> So is there a way to get the specificity of Smith Waterman in a Needlman
> Wunsch alignment ?



From Wim.DeSmet at UGent.be  Mon Apr 18 15:22:26 2011
From: Wim.DeSmet at UGent.be (Wim De Smet)
Date: Mon, 18 Apr 2011 17:22:26 +0200
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
Message-ID: <4DAC5732.5010507@UGent.be>

Hi all,

I've been trying to generate some global alignments with biojava and 
comparing them with what needle returns. Doing this, I can't seem to 
reproduce needle's alignment with biojava. The score returned from 
biojava seems to be worse than that from needle, so I'm not sure what's 
happening here.

The sequences are AB004720 and Y17238 (I didn't attach a fasta file to 
avoid spamming people, let me know if you want one). I align them with:
GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = 
Alignments.getPairwiseAligner(
new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
PairwiseSequenceAlignerType.GLOBAL,
penalty, SubstitutionMatrixHelper.getNuc4_4());
SequencePair<DNASequence, NucleotideCompound>
alignment = aligner.getPair();

This gives me an alignment with only 23% similarity and a gap at the 
end. Varying the gap penalties can give me a gap in front too, but 
that's about it. When aligning in needle, I get a sequence with a higher 
score (6784 vs (-)5862) and 94% similarity (which seems closer to home). 
Needle I just run with defaults (so it uses EDNAFULL) and a go/ge of 14/4.

Could this be a bug or am I misunderstanding some of the options?

BTW, if I use a really large gapextend, say -4000, I also get a 
nullpointer exception.

TIA,
Wim De Smet

-- 
Wim De Smet
http://www.straininfo.net/


From andreas at sdsc.edu  Mon Apr 18 18:34:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 18 Apr 2011 11:34:57 -0700
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <4DAC5732.5010507@UGent.be>
References: <4DAC5732.5010507@UGent.be>
Message-ID: <BANLkTinZuaB_vQ1iUDQshqY6k5sY7cu8LQ@mail.gmail.com>

Hi Wim,

thanks for tracking this down. I agree, something does not look right
here. I'll try to see what is going on...

Andreas

On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> Hi all,
>
> I've been trying to generate some global alignments with biojava and
> comparing them with what needle returns. Doing this, I can't seem to
> reproduce needle's alignment with biojava. The score returned from biojava
> seems to be worse than that from needle, so I'm not sure what's happening
> here.
>
> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
> spamming people, let me know if you want one). I align them with:
> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
> Alignments.getPairwiseAligner(
> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> PairwiseSequenceAlignerType.GLOBAL,
> penalty, SubstitutionMatrixHelper.getNuc4_4());
> SequencePair<DNASequence, NucleotideCompound>
> alignment = aligner.getPair();
>
> This gives me an alignment with only 23% similarity and a gap at the end.
> Varying the gap penalties can give me a gap in front too, but that's about
> it. When aligning in needle, I get a sequence with a higher score (6784 vs
> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>
> Could this be a bug or am I misunderstanding some of the options?
>
> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
> exception.
>
> TIA,
> Wim De Smet
>
> --
> Wim De Smet
> http://www.straininfo.net/
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From andreas at sdsc.edu  Wed Apr 20 17:33:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 20 Apr 2011 10:33:03 -0700
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <4DAC5732.5010507@UGent.be>
References: <4DAC5732.5010507@UGent.be>
Message-ID: <BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>

Hi Wim,

are you sure you are using the correct sequences in your test? When I
run the code at the bottom of this emails I am getting 95 and 97%
sequence ID, which is similar to what you are expecting.

Andreas

Here my code: (using latest code from SVN)

package demo;

import org.biojava3.alignment.Alignments;
import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SubstitutionMatrixHelper;
import org.biojava3.alignment.template.GapPenalty;
import org.biojava3.alignment.template.PairwiseSequenceAligner;
import org.biojava3.alignment.template.SequencePair;
import org.biojava3.core.sequence.DNASequence;
import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava3.core.sequence.compound.NucleotideCompound;

public class TestDNANeedlemanWunsch {
	public static void main(String[] args){

		String query =
"AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA"
+
		"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
		"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
		"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
		"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
		"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
		"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
		"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
		"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
		"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
		"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
		"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
		"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
		"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
		"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
		"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
		"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
		"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
		"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
		"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
		"CCCTTGTGGAGGGAGCCGGTAATTAAA";

		String target =
"CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC"
+
		"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
		"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
		"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
		"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
		"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
		"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
		"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
		"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
		"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
		"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
		"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
		"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
		"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
		"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
		"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
		"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
		"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
		"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
		"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
		"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";

		GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
Alignments.getPairwiseAligner(
				new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
				new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
				PairwiseSequenceAlignerType.GLOBAL,
				penalty, SubstitutionMatrixHelper.getNuc4_4());
		SequencePair<DNASequence, NucleotideCompound>
		alignment = aligner.getPair();
		
		System.out.println(alignment);
		
		int identical = alignment.getNumIdenticals();
		System.out.println("Number of identical residues: " + identical);
		System.out.println("% identical query: " + identical / (float)
query.length() );
		System.out.println("% identical query: " + identical / (float)
target.length() );
	}
}






On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet <Wim.DeSmet at ugent.be> wrote:
> Hi all,
>
> I've been trying to generate some global alignments with biojava and
> comparing them with what needle returns. Doing this, I can't seem to
> reproduce needle's alignment with biojava. The score returned from biojava
> seems to be worse than that from needle, so I'm not sure what's happening
> here.
>
> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
> spamming people, let me know if you want one). I align them with:
> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner =
> Alignments.getPairwiseAligner(
> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> PairwiseSequenceAlignerType.GLOBAL,
> penalty, SubstitutionMatrixHelper.getNuc4_4());
> SequencePair<DNASequence, NucleotideCompound>
> alignment = aligner.getPair();
>
> This gives me an alignment with only 23% similarity and a gap at the end.
> Varying the gap penalties can give me a gap in front too, but that's about
> it. When aligning in needle, I get a sequence with a higher score (6784 vs
> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>
> Could this be a bug or am I misunderstanding some of the options?
>
> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
> exception.
>
> TIA,
> Wim De Smet
>
> --
> Wim De Smet
> http://www.straininfo.net/
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From jayunit100 at gmail.com  Wed Apr 20 17:54:44 2011
From: jayunit100 at gmail.com (Jay Vyas)
Date: Wed, 20 Apr 2011 13:54:44 -0400
Subject: [Biojava-l] biojava resolver issues in maven
Message-ID: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>

   Hi guys, I've intermittently been getting some weird biojava/maven
resolution errors.  Any ideas on this ?

4/20/11 1:52:13 PM EDT: [WARN] Failure to transfer
org.biojava:biojava3-structure:3.0-alpha3-SNAPSHOT/maven-metadata.xml from
http://download.java.net/maven/1 was cached in the local repository,
resolution will not be reattempted until the update interval of
maven-repository.dev.java.net has elapsed or updates are forced.


From andreas at sdsc.edu  Wed Apr 20 18:04:38 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 20 Apr 2011 11:04:38 -0700
Subject: [Biojava-l] biojava resolver issues in maven
In-Reply-To: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>
References: <BANLkTi=3wOTfz3PpWfzVph3uX86q85i+aQ@mail.gmail.com>
Message-ID: <BANLkTikD1MGD5EDOt9fXZms4qfbpVKHzwQ@mail.gmail.com>

BioJava jar files are hosted at our own repository, not the public
Maven ones. It should be in your list of repositories, however if you
are setting up your own custom pom file, make sure to add:

<repositories>
 ...
	<repository>
			<id>biojava-maven-repo</id>
			<name>BioJava repository</name>
			<url>http://www.biojava.org/download/maven/</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
</repositories>

Andreas

On Wed, Apr 20, 2011 at 10:54 AM, Jay Vyas <jayunit100 at gmail.com> wrote:
> ? Hi guys, I've intermittently been getting some weird biojava/maven
> resolution errors. ?Any ideas on this ?
>
> 4/20/11 1:52:13 PM EDT: [WARN] Failure to transfer
> org.biojava:biojava3-structure:3.0-alpha3-SNAPSHOT/maven-metadata.xml from
> http://download.java.net/maven/1 was cached in the local repository,
> resolution will not be reattempted until the update interval of
> maven-repository.dev.java.net has elapsed or updates are forced.
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------



From frieman6 at gmail.com  Thu Apr 21 06:44:02 2011
From: frieman6 at gmail.com (omer f)
Date: Thu, 21 Apr 2011 09:44:02 +0300
Subject: [Biojava-l] Bio Java API - Amino Acids Data
Message-ID: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>

Hi All,

I Applied to the "Amino Acid" Project,
I found in the Bio Java API there is Amino Acids Objects,
But what i couldn't find - where there is Data (weight,Charge...) about each
Amino Acid,
My question, is there basic Data base for Amino Acids or we should get it
from user input,

Thank you,
Omer.


From Wim.DeSmet at UGent.be  Thu Apr 21 07:54:56 2011
From: Wim.DeSmet at UGent.be (Wim De Smet)
Date: Thu, 21 Apr 2011 09:54:56 +0200
Subject: [Biojava-l] comparison of the pairwise aligner to emboss' needle
In-Reply-To: <BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>
References: <4DAC5732.5010507@UGent.be>
	<BANLkTinJJ25e2rxS-gbNk6t_4_YhHmGP8g@mail.gmail.com>
Message-ID: <4DAFE2D0.7090601@UGent.be>

Hi Andreas

Thanks for having a look. I found the issue: if your sequence is lower 
case, the alignment is different. Try aligning with query.toLowerCase() 
and target.toLowerCase(), then the output is:

Number of identical residues: 334
% identical query: 0.23405746
% identical query: 0.22845417

vs upper case

Number of identical residues: 1394
% identical query: 0.9768746
% identical query: 0.95348835

So I just inserted a toUpperCase() and it works now.

Regards
Wim

On 20-04-11 19:33, Andreas Prlic wrote:
> Hi Wim,
>
> are you sure you are using the correct sequences in your test? When I
> run the code at the bottom of this emails I am getting 95 and 97%
> sequence ID, which is similar to what you are expecting.
>
> Andreas
>
> Here my code: (using latest code from SVN)
>
> package demo;
>
> import org.biojava3.alignment.Alignments;
> import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
> import org.biojava3.alignment.SimpleGapPenalty;
> import org.biojava3.alignment.SubstitutionMatrixHelper;
> import org.biojava3.alignment.template.GapPenalty;
> import org.biojava3.alignment.template.PairwiseSequenceAligner;
> import org.biojava3.alignment.template.SequencePair;
> import org.biojava3.core.sequence.DNASequence;
> import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
> import org.biojava3.core.sequence.compound.NucleotideCompound;
>
> public class TestDNANeedlemanWunsch {
> 	public static void main(String[] args){
>
> 		String query =
> "AGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGTGAAGCCCAGCTTGCTGGGTGGATCA"
> +
> 		"GTGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCCTGACTCTGGGATAAGCGCTGGAAACGGTGTCT" +
> 		"AATACTGGATATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCG" +
> 		"GCCTATCAGCTTGTTGGTGAGGTAATGGCTCACCAAGGCGTCGACGGGTAGCCGGCCTGAGAGGGTGACC" +
> 		"GGCCACACTGGGACTGAGACACGGCCCAGACTCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGC" +
> 		"GGAAGCCTGATGCAGCAACGCCGCGTGAGGGACGACGGCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAG" +
> 		"AAGCGAGAGTGACGGTACCTGCAGAAAAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAG" +
> 		"GGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAA" +
> 		"CCCGAGGCTCAACCTNNGGGCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCC" +
> 		"TGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAAC" +
> 		"TGACGCTGAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTT" +
> 		"GGGAACTAGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCACGTAACGCATTAAGTTCCCCGCCTGGGG" +
> 		"AGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTA" +
> 		"AATCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCT" +
> 		"TTGGACACTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCG" +
> 		"CAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTC" +
> 		"AACTCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACA" +
> 		"ATGGCCGGTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATT" +
> 		"GAGGTCTGCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATA" +
> 		"CGTTCCCGGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCTAA" +
> 		"CCCTTGTGGAGGGAGCCGGTAATTAAA";
>
> 		String target =
> "CTGGCCGCCTGCTTAACACATCCAAGTCGAACGGTGAAGCCCCANCTTACTGGGTGGATCAGTGCCGAAC"
> +
> 		"GGGTGAGTAACACGTGAGCAACCTCCCCCTGACTCTGGGATAAGCGCTGGAANCGGTGTCTAATACTGGA" +
> 		"TATGAGCTACCACCGCATGGTGAGTGGTTGGAAAGATTTTTCGGTTGGGGATGGGCTCGCGCCCTATGAG" +
> 		"CTTGTTGGTGAGGTAATGGCTCACCAAGCCGTCGACGGGTAGCCGGCCTGAGAGGGTGACCGNCCACACT" +
> 		"GGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCT" +
> 		"GATTCANCAACCCCGCGTGAGGGACGACGGCCTTCGGGTTGTAAACCTCTTTTAGCAGGGAAGAAGCGAG" +
> 		"AGTGACGGTACCTGCAGAAAAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCAA" +
> 		"GCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCTGTGAAAACCCGAGG" +
> 		"CTCAACCTCGGGCCTGCAGTGGGTACGGGCAGACTAGAGTGCGGTAGGGGAGATTGGAATTCCTGGTGTA" +
> 		"GCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGATCTCTGGGCCGTAACTGACGCT" +
> 		"GAGGAGCGAAAGGGTGGGGAGCAAACAGGCTTAGATACCCTGGTAGTCCACCCCGTAAACGTTGGGAACT" +
> 		"AGTTGTGGGGTCCTTTCCACGGATTCCGTGACGCAGCTAACGCATTAAGTTCCCCGCCTGGGGAGTACGG" +
> 		"CCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGCGGAGCATGCGGATTAATTCGAT" +
> 		"GCAACGCGAAGAACCTTACCAAGGCTTGACATACACGAGAACGCTGCAGAAATGTAGAACTCTTTGGACA" +
> 		"CTCGTGAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAG" +
> 		"CGCAACCCTCGTTCTATGTTGCCAGCACGTAATGGTGGGAACTCATGGGATACTGCCGGGGTCAACTCGG" +
> 		"AGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCG" +
> 		"GTACAAAGGGCTGCAATACCGTGAGGTGGAGCGAATCCCAAAAAGCCGGTCCCAGTTCGGATTGAGGTCT" +
> 		"GCAACTCGACCTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCC" +
> 		"GGGTCTTGTACACACCGCCCGTCAAGTCATGAAAGTCGGTAACACCTGAAGCCGGTGGCCCAACCCTTGT" +
> 		"GGAGGGAGCCGTCGAAGGTGGGATCGGTAATTAGGACTAAGTCGTAACAAGGTAGCCGTACC";
>
> 		GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
> 		PairwiseSequenceAligner<DNASequence, NucleotideCompound>  aligner =
> Alignments.getPairwiseAligner(
> 				new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
> 				new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
> 				PairwiseSequenceAlignerType.GLOBAL,
> 				penalty, SubstitutionMatrixHelper.getNuc4_4());
> 		SequencePair<DNASequence, NucleotideCompound>
> 		alignment = aligner.getPair();
> 		
> 		System.out.println(alignment);
> 		
> 		int identical = alignment.getNumIdenticals();
> 		System.out.println("Number of identical residues: " + identical);
> 		System.out.println("% identical query: " + identical / (float)
> query.length() );
> 		System.out.println("% identical query: " + identical / (float)
> target.length() );
> 	}
> }
>
>
>
>
>
>
> On Mon, Apr 18, 2011 at 8:22 AM, Wim De Smet<Wim.DeSmet at ugent.be>  wrote:
>> Hi all,
>>
>> I've been trying to generate some global alignments with biojava and
>> comparing them with what needle returns. Doing this, I can't seem to
>> reproduce needle's alignment with biojava. The score returned from biojava
>> seems to be worse than that from needle, so I'm not sure what's happening
>> here.
>>
>> The sequences are AB004720 and Y17238 (I didn't attach a fasta file to avoid
>> spamming people, let me know if you want one). I align them with:
>> GapPenalty penalty = new SimpleGapPenalty((short)-14, (short)-4);
>> PairwiseSequenceAligner<DNASequence, NucleotideCompound>  aligner =
>> Alignments.getPairwiseAligner(
>> new DNASequence(query, AmbiguityDNACompoundSet.getDNACompoundSet()),
>> new DNASequence(target, AmbiguityDNACompoundSet.getDNACompoundSet()),
>> PairwiseSequenceAlignerType.GLOBAL,
>> penalty, SubstitutionMatrixHelper.getNuc4_4());
>> SequencePair<DNASequence, NucleotideCompound>
>> alignment = aligner.getPair();
>>
>> This gives me an alignment with only 23% similarity and a gap at the end.
>> Varying the gap penalties can give me a gap in front too, but that's about
>> it. When aligning in needle, I get a sequence with a higher score (6784 vs
>> (-)5862) and 94% similarity (which seems closer to home). Needle I just run
>> with defaults (so it uses EDNAFULL) and a go/ge of 14/4.
>>
>> Could this be a bug or am I misunderstanding some of the options?
>>
>> BTW, if I use a really large gapextend, say -4000, I also get a nullpointer
>> exception.
>>
>> TIA,
>> Wim De Smet
>>
>> --
>> Wim De Smet
>> http://www.straininfo.net/
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>


-- 
Wim De Smet
http://www.straininfo.net/


From khalil.elmazouari at gmail.com  Thu Apr 21 10:36:29 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 12:36:29 +0200
Subject: [Biojava-l] Codon count
Message-ID: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>

Hi,

I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.

Any suggestion is welcome. 

Regards,

khalil





From ayates at ebi.ac.uk  Thu Apr 21 11:18:55 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:18:55 +0100
Subject: [Biojava-l] Bio Java API - Amino Acids Data
In-Reply-To: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>
References: <BANLkTimVgbCa03tXxFQxb2f3cCxBm-hTSQ@mail.gmail.com>
Message-ID: <4408CC30-6456-4269-B192-E9F66CEDAC3C@ebi.ac.uk>

Hi Omer,

If you are using BioJava3 then weight is available from the AminoAcidCompound object when taken from an AminoAcidCompoundSet. The other data points are not available from within BioJava. I know Andreas mentioned ages ago linking into one of the compound databases e.g. ChEBI but I don't think that's been done.

Regards,

Andy

On 21 Apr 2011, at 07:44, omer f wrote:

> Hi All,
> 
> I Applied to the "Amino Acid" Project,
> I found in the Bio Java API there is Amino Acids Objects,
> But what i couldn't find - where there is Data (weight,Charge...) about each
> Amino Acid,
> My question, is there basic Data base for Amino Acids or we should get it
> from user input,
> 
> Thank you,
> Omer.
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From ayates at ebi.ac.uk  Thu Apr 21 11:23:47 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:23:47 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
Message-ID: <C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>

Hi Khalil,

I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.

Regards,

Andy

On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:

> Hi,
> 
> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
> 
> Any suggestion is welcome. 
> 
> Regards,
> 
> khalil
> 
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From khalil.elmazouari at gmail.com  Thu Apr 21 11:37:16 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 13:37:16 +0200
Subject: [Biojava-l] Codon count
In-Reply-To: <C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
Message-ID: <1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>

Thanks Andy,
it's the second option I am looking for.

Regards,
khalil



On 21 Apr 2011, at 13:23, Andy Yates wrote:

> Hi Khalil,
> 
> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
> 
> Regards,
> 
> Andy
> 
> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
> 
>> Hi,
>> 
>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>> 
>> Any suggestion is welcome. 
>> 
>> Regards,
>> 
>> khalil
>> 
>> 
>> 
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 




From ayates at ebi.ac.uk  Thu Apr 21 11:40:00 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 12:40:00 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
Message-ID: <6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>

Hi Khalil,

Then I think windowed sequence is the only way to go. Actually one particularly "interesting" idea has just sprung to mind. What if you translated the entire sequence in frame 1 forward & reverse? Then finding the amount of correct codons is a case of looking for amino acids which are not a stop or unknown amino acid.

Andy

On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:

> Thanks Andy,
> it's the second option I am looking for.
> 
> Regards,
> khalil
> 
> 
> 
> On 21 Apr 2011, at 13:23, Andy Yates wrote:
> 
>> Hi Khalil,
>> 
>> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
>> 
>> Regards,
>> 
>> Andy
>> 
>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>> 
>>> Hi,
>>> 
>>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>>> 
>>> Any suggestion is welcome. 
>>> 
>>> Regards,
>>> 
>>> khalil
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> -- 
>> Andrew Yates                   Ensembl Genomes Engineer
>> EMBL-EBI                       Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>> 
>> 
>> 
>> 
> 

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From khalil.elmazouari at gmail.com  Thu Apr 21 11:54:23 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Thu, 21 Apr 2011 13:54:23 +0200
Subject: [Biojava-l] Codon count
In-Reply-To: <6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
	<6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
Message-ID: <7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>

Hi Andy,

I am actually counting codons via 6 ORFs translations. I am working on ?100.000 seq/run => 600.000 ORFs to check. So, performance is an issue for my job.

I am just wondering if counting Codons directly on NT seq (both strand) will be faster vs translation + AA counting.

Regards,

khalil


On 21 Apr 2011, at 13:40, Andy Yates wrote:

> Hi Khalil,
> 
> Then I think windowed sequence is the only way to go. Actually one particularly "interesting" idea has just sprung to mind. What if you translated the entire sequence in frame 1 forward & reverse? Then finding the amount of correct codons is a case of looking for amino acids which are not a stop or unknown amino acid.
> 
> Andy
> 
> On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:
> 
>> Thanks Andy,
>> it's the second option I am looking for.
>> 
>> Regards,
>> khalil
>> 
>> 
>> 
>> On 21 Apr 2011, at 13:23, Andy Yates wrote:
>> 
>>> Hi Khalil,
>>> 
>>> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
>>> 
>>> Regards,
>>> 
>>> Andy
>>> 
>>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>>>> 
>>>> Any suggestion is welcome. 
>>>> 
>>>> Regards,
>>>> 
>>>> khalil
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>> 
>>> -- 
>>> Andrew Yates                   Ensembl Genomes Engineer
>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>> 
>>> 
>>> 
>>> 
>> 
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 




From ayates at ebi.ac.uk  Thu Apr 21 12:06:35 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 13:06:35 +0100
Subject: [Biojava-l] Codon count
In-Reply-To: <7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>
References: <7348CEDD-3D91-4351-A24E-130B4D72DAE8@gmail.com>
	<C7C0DDDA-DDAD-4879-8EE0-477EC9E1CF94@ebi.ac.uk>
	<1DECE13D-34A1-4EFC-ADED-320395E9320A@gmail.com>
	<6E526B83-5E96-4364-A248-9270FE139D7D@ebi.ac.uk>
	<7DFE6B97-A465-4A1A-8EC6-A6BEC1EFCBF3@gmail.com>
Message-ID: <6177ca65-9f8b-40bb-8856-03bf6ad62361@email.android.com>

There will be a performance hit but you'll be rewriting the translation code so maybe the speed reduction isn't worth the recoding task. Give it a benchmark before recoding. I can't remember the exact speed but it isn't too slow

Andy

Khalil El Mazouari <khalil.elmazouari at gmail.com> wrote:

>Hi Andy,
>
>I am actually counting codons via 6 ORFs translations. I am working on
>?100.000 seq/run => 600.000 ORFs to check. So, performance is an issue
>for my job.
>
>I am just wondering if counting Codons directly on NT seq (both strand)
>will be faster vs translation + AA counting.
>
>Regards,
>
>khalil
>
>
>On 21 Apr 2011, at 13:40, Andy Yates wrote:
>
>> Hi Khalil,
>> 
>> Then I think windowed sequence is the only way to go. Actually one
>particularly "interesting" idea has just sprung to mind. What if you
>translated the entire sequence in frame 1 forward & reverse? Then
>finding the amount of correct codons is a case of looking for amino
>acids which are not a stop or unknown amino acid.
>> 
>> Andy
>> 
>> On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote:
>> 
>>> Thanks Andy,
>>> it's the second option I am looking for.
>>> 
>>> Regards,
>>> khalil
>>> 
>>> 
>>> 
>>> On 21 Apr 2011, at 13:23, Andy Yates wrote:
>>> 
>>>> Hi Khalil,
>>>> 
>>>> I'm not 100% sure what you want here. If you just want to know the
>potential number of codons on both strands of DNA then it would be
>(length / 3)*2. If what you are actually asking for is how many codons
>code for an amino acid then you would have to perform work similar to
>the transcription engine in BJ3. All codon tables are available from
>the IUPACParser class & then it would be up to you to use a
>WindowedSequence over the top of your NT sequence to get the windows or
>SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the
>WindowedSequence.
>>>> 
>>>> Regards,
>>>> 
>>>> Andy
>>>> 
>>>> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I am looking for a simple method or class to count the number of a
>specific AA codon on NT seq. Counting on both strands.
>>>>> 
>>>>> Any suggestion is welcome. 
>>>>> 
>>>>> Regards,
>>>>> 
>>>>> khalil
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>> 
>>>> -- 
>>>> Andrew Yates                   Ensembl Genomes Engineer
>>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>> 
>> -- 
>> Andrew Yates                   Ensembl Genomes Engineer
>> EMBL-EBI                       Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>> 
>> 
>> 
>> 



From flf.mib at gmail.com  Thu Apr 21 21:18:01 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Thu, 21 Apr 2011 23:18:01 +0200
Subject: [Biojava-l] translation and leucine
Message-ID: <4DB09F09.4060303@gmail.com>

Dear all,
i have a quick question about translation with biojava 3

I would like to retrieve that the codon CTA is coding for a leucine.
But some leucine codons code also for a start in Universal Genetic code

Here I have build a very short example:
given  a short dna sequence coomposed of a start codon and 6 leucine codons

TranscriptionEngine e = TranscriptionEngine.getDefault();
DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
//return MLLLLLL : OK

DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
//return MLLLLLL : KO I would prefer have LLLLLLL !

DNASequence dd = new DNASequence("CTA");
//return M : KO I would prefer have L !

Could someone explain me this feature ?
How the default transcritionEngine works?

How can I ask to the TranscriptionEngine give me the aminoacids 
corresponding to CTA when it is not in first position?

Thanks a lot for your help !

Francois



From ayates at ebi.ac.uk  Thu Apr 21 21:46:14 2011
From: ayates at ebi.ac.uk (Andy Yates)
Date: Thu, 21 Apr 2011 22:46:14 +0100
Subject: [Biojava-l] translation and leucine
In-Reply-To: <4DB09F09.4060303@gmail.com>
References: <4DB09F09.4060303@gmail.com>
Message-ID: <44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>

Hi Francois,

The engine by default will always return the first amino acid as an init met if the amino acid could have been a start codon (but stupid atmo but it will be altered). If you do not want this behaviour then you'll have to create your own. You can do this using the following:

TranscriptionEngine e = new TranscriptionEngine.Builder().initMet(false).build();

HTH,

Andy

On 21 Apr 2011, at 22:18, Fran?ois Le F?vre wrote:

> Dear all,
> i have a quick question about translation with biojava 3
> 
> I would like to retrieve that the codon CTA is coding for a leucine.
> But some leucine codons code also for a start in Universal Genetic code
> 
> Here I have build a very short example:
> given  a short dna sequence coomposed of a start codon and 6 leucine codons
> 
> TranscriptionEngine e = TranscriptionEngine.getDefault();
> DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
> //return MLLLLLL : OK
> 
> DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
> //return MLLLLLL : KO I would prefer have LLLLLLL !
> 
> DNASequence dd = new DNASequence("CTA");
> //return M : KO I would prefer have L !
> 
> Could someone explain me this feature ?
> How the default transcritionEngine works?
> 
> How can I ask to the TranscriptionEngine give me the aminoacids corresponding to CTA when it is not in first position?
> 
> Thanks a lot for your help !
> 
> Francois
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/







From flf.mib at gmail.com  Sat Apr 23 06:12:53 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Sat, 23 Apr 2011 08:12:53 +0200
Subject: [Biojava-l] translation and leucine
In-Reply-To: <44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>
References: <4DB09F09.4060303@gmail.com>
	<44E003C7-40C8-4595-BCAC-1613C296FFEC@ebi.ac.uk>
Message-ID: <4DB26DE5.8000805@gmail.com>

Andy
ok, perfect I did not know it!
Thanks
Francois
> Hi Francois,
>
> The engine by default will always return the first amino acid as an init met if the amino acid could have been a start codon (but stupid atmo but it will be altered). If you do not want this behaviour then you'll have to create your own. You can do this using the following:
>
> TranscriptionEngine e = new TranscriptionEngine.Builder().initMet(false).build();
>
> HTH,
>
> Andy
>
> On 21 Apr 2011, at 22:18, Fran?ois Le F?vre wrote:
>
>> Dear all,
>> i have a quick question about translation with biojava 3
>>
>> I would like to retrieve that the codon CTA is coding for a leucine.
>> But some leucine codons code also for a start in Universal Genetic code
>>
>> Here I have build a very short example:
>> given  a short dna sequence coomposed of a start codon and 6 leucine codons
>>
>> TranscriptionEngine e = TranscriptionEngine.getDefault();
>> DNASequence dd = new DNASequence("ATGTTGTTACTTCTCCTACTG");
>> //return MLLLLLL : OK
>>
>> DNASequence dd = new DNASequence("CTATTGTTACTTCTCCTACTG");
>> //return MLLLLLL : KO I would prefer have LLLLLLL !
>>
>> DNASequence dd = new DNASequence("CTA");
>> //return M : KO I would prefer have L !
>>
>> Could someone explain me this feature ?
>> How the default transcritionEngine works?
>>
>> How can I ask to the TranscriptionEngine give me the aminoacids corresponding to CTA when it is not in first position?
>>
>> Thanks a lot for your help !
>>
>> Francois
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l



From rmb32 at cornell.edu  Mon Apr 25 21:42:48 2011
From: rmb32 at cornell.edu (Robert Buels)
Date: Mon, 25 Apr 2011 14:42:48 -0700
Subject: [Biojava-l] Announcing OBF Google Summer of Code Accepted Students
Message-ID: <4DB5EAD8.1020905@cornell.edu>

Hello all,

I'm very pleased and excited to announce that the Open Bioinformatics 
Foundation has selected 6 very capable students to work on OBF projects 
this summer as part of the Google Summer of Code program.

The accepted students, their projects, and their mentors (in 
alphabetical order):

Justinas Vygintas Daugmaudis
Michele dos Santos da Silva
    (2 students!)
    Mocapy++Biopython: from data to probabilistic models of biomolecules
    mentored by Thomas Hamelryck and Eric Talevich

Chuan Hock Koh
   BioJava - Amino acids physico-chemical properties calculation
   mentored by Peter Troshin, Andreas Prlic, and Jay Vyas

Micha? Koziarski
    Representing bio-objects and related information with images
    (BioRuby)
    mentored by Raoul J.P. Bonnal and Francesco Strozzi

Sheena Scroggins
    Major BioPerl Reorganization
    mentored by Robert Buels and Chris Fields

Mikael Eric Trellet
    Interface analysis module for BioPython
    mentored by Jo?o Rodrigues and Eric Talevich


Once again this year, we received many great applications and ideas. 
However, funding and mentor resources are limited, and we were not able 
to accept as many as we would have liked.  Our deepest thanks to all the 
students who applied: we sincerely appreciate the time and effort you 
put into your applications, and hope you will still consider being a 
part of the OBF's open source projects, even without Google funding.  I 
speak for myself and all of the mentors who read and scored applications 
when I say that we were truly honored by the number and quality of the 
applications we received.

For the accepted students: congratulations!  You have risen to the top 
of a very competitive application process.  Now it's time to "put your 
money where your mouth is", as the saying goes.  Let's get out there and 
write some great code this summer!

Best regards,

Rob

----
Robert Buels
OBF GSoC 2011 Administrator


From pavlo.lutsik at googlemail.com  Tue Apr 26 11:07:42 2011
From: pavlo.lutsik at googlemail.com (Pavlo Lutsik)
Date: Tue, 26 Apr 2011 13:07:42 +0200
Subject: [Biojava-l] NCBIQBlastService
Message-ID: <op.vujk64qq4c6xo5@plus-laptop-win.funklan.uni-saarland.de>


Hi,

cannot get the subject class working in the Cookbook example. Simple  
rbw.printRemoteBlastInfo() throws the

java.lang.Exception: Impossible to get info from QBlast service at this  
time. Check your network connection.

Any ideas?

Best,
Pavlo Lutsik


From p.v.troshin at dundee.ac.uk  Wed Apr 27 13:49:54 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 27 Apr 2011 14:49:54 +0100
Subject: [Biojava-l] amino acid physico-chemical properties calculation
	project
In-Reply-To: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
References: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
Message-ID: <4DB81F02.2020504@dundee.ac.uk>

Dear students,

I would like to thank all of you for your interest in and enthusiasm for 
the amino acid physico-chemical properties calculation project 2011 
Google Summer of Code. Unfortunately, only one student has to be chosen 
and I am sorry if this happens not to be you.

This idea generated enormous interest and we have received a total of 18 
applications for this idea. Many of those are of good or very good 
quality. I worked with many of you during the application process, and 
was very impressed by the level of enthusiasm, energy, and capability I 
saw in the applications and our conversations on the mailing list.

It wasn't easy to choose the best applicant, but we had to do it.

A few general comments on the solutions for the short coding exercise.

1) Make sure you understand the task. About half of the application 
fails to stick to the specifications.

2) Only a few people used threads correctly. Among them only one person 
used java.concurrency package, which I expected everyone to use. I would 
recommend reading B.Goetz "Java Concurrency in Practice" if you want to 
learn more about multithreading in Java.

3) Do not overcomplicate the solution; good programmer would do just 
what he was asked to.

4) You can determine whether your solution worked correctly by 
processing the following input

aaabbbccc    bbcccalkfw
aaaabb    aaabbbcc
caaabbbccc    aaabbbccc
aaaaabbbbb    abbbbbccdddd
sjdhfjksdhfk    weiuriweiru
ddddrepeatrepeat    repeatrepeat

and comparing it to the output that should have been produced:

aaab
a
c
aaaa
sjdhfjksdhfk
dddd

Thanks to everyone again, and I wish you all the best of luck with 
whatever endeavour you take on.

Regards,
Peter




On 26/04/2011 07:33, Alexandru Paiu wrote:
>  Hi Peter .
>
>  I want to know what should I improve in the next gsoc . I wan't to
>  know what wasn't right for my application .
>
>  In my opinion I think that I did a good job with the solutions for
>  instability index and isoelectric point which are the hardest methods
>  . I even used the jay vyas suggestion with those hashtables .
>
>  Please , give me an advice
>
>  Best regards Paiu Alexandru




From p.v.troshin at dundee.ac.uk  Wed Apr 27 14:05:42 2011
From: p.v.troshin at dundee.ac.uk (Peter Troshin)
Date: Wed, 27 Apr 2011 15:05:42 +0100
Subject: [Biojava-l] Please give me an advice
In-Reply-To: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
References: <BANLkTi=EmBtVhw6EmNqaitSmE1f7rJdLMg@mail.gmail.com>
Message-ID: <4DB822B6.9030003@dundee.ac.uk>

Dear Alex,

There was nothing particularly wrong with your project plan, it just was 
not as good as the winning proposal. Your solution for the coding 
exercise did not run out of the box (java -jar runme.jar), was not 
correct and could have been better engineered.

I'd recommend you to contribute to the open source project of your 
choice before applying to the GSoC next year. This way you will be in a 
much better position for the next GSoC.

Regards,
Peter

On 26/04/2011 07:33, Alexandru Paiu wrote:
> Hi Peter .
>
> I want to know what should I improve in the next gsoc . I wan't to 
> know what wasn't right for my application .
>
> In my opinion I think that I did a good job with the solutions for 
> instability index and isoelectric point which are the hardest methods 
> . I even used the jay vyas suggestion with those hashtables .
>
> Please , give me an advice
>
> Best regards
> Paiu Alexandru



From flf.mib at gmail.com  Wed Apr 27 19:54:28 2011
From: flf.mib at gmail.com (=?ISO-8859-1?Q?Fran=E7ois_Le_F=E8vre?=)
Date: Wed, 27 Apr 2011 21:54:28 +0200
Subject: [Biojava-l] biojava3 and blast xml parser
Message-ID: <4DB87474.1080307@gmail.com>

Dear all,

I have just a difficulty: is there still a blast xml parser in the 
biojava 3.0-SNAPSHOT
I am not able to find it...

I have found
http://www.biojava.org/docs/api1.8/org/biojava/bio/program/sax/blastxml/BlastXMLParser.html
with a good tutorial here
http://biojava.org/wiki/BioJava:CookBook:Blast:Echo

but it seems to be part of biojava 1.8

can you confirm me?

Thanks

Francois



From willishf at ufl.edu  Wed Apr 27 21:30:52 2011
From: willishf at ufl.edu (Scooter Willis)
Date: Wed, 27 Apr 2011 17:30:52 -0400
Subject: [Biojava-l] biojava3 and blast xml parser
In-Reply-To: <4DB87474.1080307@gmail.com>
References: <4DB87474.1080307@gmail.com>
Message-ID: <BANLkTimozSz2U4pV6sDj=WfvkfPmspgZ=w@mail.gmail.com>

We did not migrate the blast xml parser from 1.8 to 3.0. Typically I
will load the XML as a DOM object and use xpath to query the desired
results. I have some code in the biojava3-genome module
(org.biojava3.genome.BlastXMLQuery) that could possibly provide a
solution for you depending on what you are trying to accomplish. Let
me know if you have specific requirements that could help motivate
formal blast XML->Java objects support in Biojava3.

Thanks

Scooter

2011/4/27 Fran?ois Le F?vre <flf.mib at gmail.com>:
> Dear all,
>
> I have just a difficulty: is there still a blast xml parser in the biojava
> 3.0-SNAPSHOT
> I am not able to find it...
>
> I have found
> http://www.biojava.org/docs/api1.8/org/biojava/bio/program/sax/blastxml/BlastXMLParser.html
> with a good tutorial here
> http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
>
> but it seems to be part of biojava 1.8
>
> can you confirm me?
>
> Thanks
>
> Francois
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>