From salmantahir1 at gmail.com  Tue Feb  6 06:21:41 2007
From: salmantahir1 at gmail.com (Salman Tahir)
Date: Tue, 6 Feb 2007 11:21:41 +0000
Subject: [Biojava-l] Variable modifications to Protein sequences
Message-ID: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>

Hi,

I am emailing regarding a java program that I am writing which deals with
the in silico manipulation of cross-linked peptides.

I would like to manipulate protein sequences by taking into account variable
modifications using BioJava classes (if possible). For example:

If I have the following variable modification:
hydroxo-BS2GD4 (N-term, K): 118.0563805

And the following sequence: FLEKQNKER (assuming it contains the N-term)

I need to generate the following sequences
FLEKQNKER -> FLEKQNKER, FLEKhydroxo-BS2GD0QNKER, FLEKQNKhydroxo-BS2GD0ER,
FLEKhydroxo-BS2GD0QNKhydroxo-BS2GD0 ER, Fhydroxo-BS2GD0LEK QNKER and so on -
generating a total of 8 peptide sequences with different masses.

Is there a way i can generate these additional sequences using BioJava? Any
help would be mostly appreciated.

- Salman

From markjschreiber at gmail.com  Wed Feb  7 10:30:47 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 7 Feb 2007 23:30:47 +0800
Subject: [Biojava-l] Variable modifications to Protein sequences
In-Reply-To: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>
References: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>
Message-ID: <93b45ca50702070730n79d0aea2seefa3f3af5cebd1@mail.gmail.com>

Hi -
I think that the best approach would be to define your own custom
alphabet (possibly with a custom tokenization). You could then create
SymbolLists or sequences with this new alphabet.
- Mark

On 2/6/07, Salman Tahir <salmantahir1 at gmail.com> wrote:
> Hi,
>
> I am emailing regarding a java program that I am writing which deals with
> the in silico manipulation of cross-linked peptides.
>
> I would like to manipulate protein sequences by taking into account variable
> modifications using BioJava classes (if possible). For example:
>
> If I have the following variable modification:
> hydroxo-BS2GD4 (N-term, K): 118.0563805
>
> And the following sequence: FLEKQNKER (assuming it contains the N-term)
>
> I need to generate the following sequences
> FLEKQNKER -> FLEKQNKER, FLEKhydroxo-BS2GD0QNKER, FLEKQNKhydroxo-BS2GD0ER,
> FLEKhydroxo-BS2GD0QNKhydroxo-BS2GD0 ER, Fhydroxo-BS2GD0LEK QNKER and so on -
> generating a total of 8 peptide sequences with different masses.
>
> Is there a way i can generate these additional sequences using BioJava? Any
> help would be mostly appreciated.
>
> - Salman
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From su24 at st-andrews.ac.uk  Wed Feb  7 11:11:37 2007
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Wed,  7 Feb 2007 16:11:37 +0000
Subject: [Biojava-l] Use Of Blosum62
Message-ID: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>


Dear All,

I am having a problem using the Blosum62 matrix file from the NCBI website for
use in Smith-Waterman alignments. When I attempt to run my code reading in the
file to initialise the Substitution Matrix Object the following exception is
thrown

"org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
contain character: '*'"



Thanking you in advance,

Saif



--------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Sir Harold Mitchell Building
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk


From su24 at st-andrews.ac.uk  Wed Feb  7 11:38:52 2007
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Wed,  7 Feb 2007 16:38:52 +0000
Subject: [Biojava-l] Use Of Blosum62
In-Reply-To: <45C9FD73.5040200@ebi.ac.uk>
References: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>
	<45C9FD73.5040200@ebi.ac.uk>
Message-ID: <1170866332.45ca009c26757@webmail.st-andrews.ac.uk>

Hi,

Here is the code I am using


Cheers,

Saif

public static void main(String args[])
	{
		String x=("prot sequence excluded");
		String y=("prot sequence excluded");

		try {

	      FiniteAlphabet alphabet
(FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");

SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet, new
File("///Users/su24/BLOSUM62"));

// The above line causes the exception

	      SequenceAlignment  aligner = new SmithWaterman( -1,3,2,2,1,matrix);
	      Sequence query  = ProteinTools.createProteinSequence(x, "query");
	      Sequence target = ProteinTools.createProteinSequence(y, "target");
	      aligner.pairwiseAlignment(query, target);


	      System.out.println("\nlocal alignment with SmithWaterman:\n" +
aligner.getAlignmentString());
	    }

	catch (Exception exc) {
	      exc.printStackTrace();
	    }
	  }


	}

Quoting Richard Holland <holland at ebi.ac.uk>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi. You need to include your complete program code in your email so that
> we can accurately diagnose the problem.
>
> cheers,
> Richard
>
> Saif Ur-Rehman wrote:
> > Dear All,
> >
> > I am having a problem using the Blosum62 matrix file from the NCBI website
> for
> > use in Smith-Waterman alignments. When I attempt to run my code reading in
> the
> > file to initialise the Substitution Matrix Object the following exception
> is
> > thrown
> >
> > "org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
> > contain character: '*'"
> >
> >
> >
> > Thanking you in advance,
> >
> > Saif
> >
> >
> >
> >
>
--------------------------------------------------------------------------------
> > Saif Ur-Rehman
> > Research Student
> > The Centre for Evolution, Genes & Genomics (CEGG)
> > Sir Harold Mitchell Building
> > School of Biology
> > The University of St Andrews
> > St Andrews,
> > Fife
> > Scotland,UK
> >
> > ------------------------------------------------------------------
> > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFFyf1y4C5LeMEKA/QRAp7zAJ9ncsgYyBBRDrgSBnANTYv0xYI+PwCgpGv0
> cQQ8vFVB8QtKW9kAt9pRSEQ=
> =2rLL
> -----END PGP SIGNATURE-----
>


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Sir Harold Mitchell Building
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk


From andreas.draeger at uni-tuebingen.de  Wed Feb  7 13:15:59 2007
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Wed, 07 Feb 2007 19:15:59 +0100
Subject: [Biojava-l] Use Of Blosum62
In-Reply-To: <1170866332.45ca009c26757@webmail.st-andrews.ac.uk>
References: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>	<45C9FD73.5040200@ebi.ac.uk>
	<1170866332.45ca009c26757@webmail.st-andrews.ac.uk>
Message-ID: <45CA175F.1050105@uni-tuebingen.de>

Hey Saif,

> 	      FiniteAlphabet alphabet
> (FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");
> 

This cannot work because the symbol "*" is indeed not included in the 
alphabet "PROTEIN" as it marks the termination symbol. You will need to 
use the alphabet "PROTEIN-TERM".
I hope that helps.
If I remember correctly, there have been discussions about that special 
character in previous e-mails on that list.

Cheers,
Andreas

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091

From Russell.Smithies at agresearch.co.nz  Sun Feb 11 19:55:17 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 12 Feb 2007 13:55:17 +1300
Subject: [Biojava-l] New Zealand bioinformatician vacancy
In-Reply-To: <6dce9a0b0702110814v16d50c5dtc1c8c6f21f14c450@mail.gmail.com>
References: <1170950909.6074.30.camel@localhost><6dce9a0b0702081123j3e8efe89r4e2a93b88d4029d9@mail.gmail.com><1170967751.6084.18.camel@localhost><6dce9a0b0702081307s11683737r17e8d22b47ed6fef@mail.gmail.com><1170970046.6084.36.camel@localhost><6dce9a0b0702081552n28e0aa79x79a8d4eb659fe119@mail.gmail.com><1171105304.5853.11.camel@localhost>
	<6dce9a0b0702110814v16d50c5dtc1c8c6f21f14c450@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C04AC32D2@imail.agresearch.co.nz>

Hi all,

I hope you don't mind me posting an advert but we have an opening for a
bioinformatician.

So if you'd like to work in New Zealand, read on...

 

thanx,

Russell

Russell Smithies 
Bioinformatics Software Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

AgResearch Farming Food and Health. First 
Te Ahuwhenua, Te Kai me te Whai Ora. Tuatahi 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 

 ========================================================== 

 

 

 Bioinformatician

AgResearch - Applied Biotechnologies

 

As part of AgResearch's company strategy we are continuing to grow our
business in the area of bioinformatics.  This capability is essential
for our science discovery.

 

In this position you will be part of a national team of 26
bioinformaticians, mathematical biologists and statisticians and be
based at our Grasslands campus at Palmerston North.  This is a permanent
position.

 

You will be an advocate for bioinformatics within AgResearch; you will
work collaboratively on projects and will provide bioinformatics
training and advice to science staff working in the biotechnology area.

 

We are seeking a person who has:

*               An excellent tertiary qualification in molecular biology
or genetics

*               Experience with the use of bioinformatics applications

*               Knowledge of life sciences databases and the internet

*               Well developed IT technical skills and web based
technologies

*               Experience in a training environment

*               Excellent writing, speaking and interpersonal skills

*               Familiarity with Perl, Java or Unix Scripting

 

If you possess the above skills, we would like to hear from you.

 

To find out more about this position please contact Peter Johnstone by
email peter.johnstone at agresearch.co.nz or alternatively phone +64 3 489
9081.

 

For a job description and to apply on line please go to
http://www.agresearch.co.nz/recruitment .  Vacancy No AGR494.  Please
provide contact details for 2 Referees with your application.

 

For general information on AgResearch please visit our website at
www.agresearch.co.nz <http://www.agresearch.co.nz/> 

 

Applications close 9th March 2007.

 

Linda Murray

Science Administrator

AgResearch Limited

Invermay Agricultural Centre

Private Bag 50034

Mosgiel, New Zealand

Phone: +64 3 489 9011

Email:  linda.murray at agresearch.co.nz 


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
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=======================================================================


From salmantahir1 at gmail.com  Mon Feb 12 05:41:40 2007
From: salmantahir1 at gmail.com (Salman Tahir)
Date: Mon, 12 Feb 2007 10:41:40 +0000
Subject: [Biojava-l] Tokenization
Message-ID: <2049e51a0702120241k135a92edl235910394f1d124c@mail.gmail.com>

Hi,

I've created a custom alphabet and I would like to use it to parse a file.
After defining the symbols in the alphabet I do the following:

SymbolTokenization parser = alpha.getTokenization("token");

('alpha being the custom alphabet'). However I get the following error:

"BioException: There is no tokenization 'token' defined in alphabet Variable
Modifications"

I understand this to mean that I have to populate the new tokenization
appropriately because this is a new alphabet. However, I cannot find any
examples that show how to achieve this. Can anyone help?

- Salman

From m.titulaer at erasmusmc.nl  Wed Feb 14 10:38:58 2007
From: m.titulaer at erasmusmc.nl (Mark Titulaer)
Date: Wed, 14 Feb 2007 16:38:58 +0100
Subject: [Biojava-l] Conversion Applied Bioisystems MALDI Voyager DE-STR
 .dat file into peak list
Message-ID: <45D32D12.3070800@erasmusmc.nl>

I would like to convert an Applied Biosystems  MALDI Voyager DE-STR  
.dat file into a peak list.
Is there any library available ?





From paolo.romano at istge.it  Tue Feb 20 05:39:30 2007
From: paolo.romano at istge.it (Paolo Romano)
Date: Tue, 20 Feb 2007 11:39:30 +0100
Subject: [Biojava-l] Final Call for Papers NETTAB 2007
Message-ID: <7.0.1.0.0.20070220113922.01e9c968@istge.it>

=================================
Apologies, if you're receiving multiple copies
=================================

Final Call for Papers

7th International Workshop NETTAB 2007
June 12-15, 2006
Department of Computer Science, University of Pisa, Pisa
http://www.nettab.org/2007/

FOCUS THEME
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications

ADJUNCT THEMES
Algorithms in bioinformatics
Formal Methods for Systems Biology
Network Tools and Applications in Bioinformatics

AIMS
This workshop aims at getting together 
biologists, bioinformaticians, computer 
scientists and linguists to try to answer the following questions:
- Is the Semantic Web of some use for Bioinformatics?
- Which goals should have a Semantic Web for Bioinformatics?
- Which standards, technologies and tools of the 
Semantic Web can most profitably be used in Bioinformatics?
- Which application did the Semantic Web already find in Bioinformatics?
- Which current Bioinformatics research problems 
can be solved by the Semantic Web?
- Which are the short, medium and long term 
perspectives in applying Semantic Web technologies to Bionformatics?

The workshop also intends to:
- introduce the basic knowledge of related 
standards and technologies, in a non trivial way 
through invited lectures and tutorials
- outline the promising features of the Semantic 
Web in bioinformatics through invited lectures and open discussion
- show some valuable examples in bioinformatics 
through invited lectures, oral communications and posters
- support as much discussion as possible through 
open discussions and a panel discussion
- practically demonstrate "how it works" through tutorials

INVITED SPEAKERS
We are extremely glad to inform you that four 
excellent speakers have accepted to give an 
invited lecture at next NETTAB workshop.
+ Session on Goals of the Semantic Web in Bioinformatics
    Invited speaker: Eric Neumann, Co-chair of 
the Health Care and Life Science Interest Group 
of the Semantic Web Activity at W3C & Teranode Inc., USA
+ Session on Semantic Web Standards and Technologies
    Invited speaker: Guus Schreiber, Chair of 
Semantic Web Deployment Interest Group at W3C & 
University of Amsterdam, The Netherlands
+ Session on Semantic Web Tools
    Invited speaker: Olivier Bodenreider, Medical 
Ontology Research, National Library of Medicine, USA
+ Session on Applications of Semantic Web in Bioinformatics
    Invited speakers: Michael Schroeder, Biotec 
TU Dresden, Germany, and Albert Burger, Heriot-Watt University, Scotland, UK
Titles of the lectures will soon be announced.

TOPICS
NETTAB workshops also include general sessions on 
Network Tools and Applications in Biology and 
adjunct focus topics selected by local organizers.
You are therefore welcome to submit your work on any of the followings topics:

Goals of a Semantic Web for Bioinformatics:
Standards, Technologies, Tools for the Semantic Web
Systems for a Semantic Web for Bioinformatics:
Existing and perspective applications of the Semantic Web for Bioinformatics

Algorithms in Bioinformatics
Formal Methods for Systems Biology
Network Tools and Applications in Bioinformatics

DEADLINES
Submission of oral communications: March 16, 2007
Proposals for tutorials: March 16, 2007
Submission of posters: April 20, 2007
Early Registration Deadline: April 27, 2007

SUBMISSION OF CONTRIBUTIONS
You are welcome to submit your contributions 
through the MyReview system at the following URL: 
http://www.nettab.org/2007/myreview/ .
This is a two steps submission procedure. You 
will have to submit first an abstract and later the paper.
You are invited to prepare your contribution 
according to instructions available at 
http://www.biomedcentral.com/bmcbioinformatics/ifora/ 
(specially, see "Preparing main manuscript text" section).
See the workshop's web site for more details 
about the preparation of the papers.

PUBLICATION OF PAPERS AND POSTERS
All accepted oral communications and posters will 
be published in the Workshop's Proceedings that 
will be distributed to all participants.
Selected papers will be published by BMC Bioinformatics as a Supplement Issue.
When submitting, you will be asked if your 
submission is intended for the workshop only or 
for the publication in BMC Bioinformatics too.
The papers will be reviewed by the members of the 
Programme Committee. They will decide whether the 
papers are accepted for the workshop only or for 
the publication in BMC Bioinformatics as well.
The workshop will engage itself to pay part of 
the cost of the publication, but please be 
advised that depending on the final budget of the 
workshop you could be requested to contribute to 
publication costs which has been set to 600 British pounds per paper.
For any further information or clarification, 
please contact the organization by email at info at nettab.org .

CHAIRS
P. Romano, Bioinformatics, Natl Cancer Research Inst., Italy
M. Schr?der, Biotechnology Centre, TU Dresden, Germany
N. Cannata, Mathematics & Computer Science Dept, Univ. of Camerino, Italy
O. Signore, ISTI, National Research Council, Italy

PROGRAMME COMMITTEE
G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT
C. Baker, Institute for Infocomm Research (I2R), SG
P. Barahona, Department of Informatics, New University of Lisboa, PT
L. Barrio-Alvers, Transinsight GmbH, DE
O. Bodenreider, National Library of Medicine, USA
A. Burger, Department of Computer Science, Heriot-Watt University, UK
M. Cannataro, Experimental and Clinical Medicine 
Dept, Univ. of Catanzaro "Magna Graecia", IT
W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA
M. Cockerill, BioMed Central, UK
M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR
R. Dieng, INRIA, Sophia Antipolis, FR
L. Grivell, European Molecular Biology Organisation, DE
M. Harris, European Bioinformatics Institute, UK
M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT
C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT
J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK
M. Krallinger, Spanish National Cancer Research Center (CNIO), ES
L. Krippahl, Department of Informatics, New University of Lisboa, PT
P. Lambrix, Computer and Information Science Dept, Link?ping University, SE
U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE
J. Luciano, Department of Genetics, Harvard Medical School, USA
R. Marangoni, Computer Science Department, University of Pisa, IT
M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT
M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT
G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT
E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT
S. Moeller, Institute of Neuro- and Bioinformatics, University of L?beck, DE
S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE
D. Quann, IBM Software Group, USA
D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA
S.-A. Sansone, European Bioinformatics Institute, UK
M. Senger, International Rice Research Institute, PH
D. Turi, School of Computer Science, University of Manchester, UK
G. Vetere, IBM Center for Advanced Studies of Rome, IT
D. Zaccagnini, Language and Computing, USA

Looking forward to seeing you all in Tuscany.

Best regards.

On behalf of the Chairs and of the Organizing Committee

Paolo Romano

Paolo Romano (paolo.romano at istge.it)
Bioinformatics and Structural Proteomics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295



From kumar at neb.com  Wed Feb 21 16:33:48 2007
From: kumar at neb.com (Sanjay Kumar)
Date: Wed, 21 Feb 2007 16:33:48 -0500
Subject: [Biojava-l] Job opportunity - Bioinformatics Software Developer
Message-ID: <C20224EC.2AA1%kumar@neb.com>

Hi-

Sorry for the job posting, but NEB has an opening for a bioinformatics
software developer that might be just right for someone with BioJava
experience. We are located just north of Boston Massachusetts, USA, and the
work environment is wonderful.

The posting is listed below and at our web site:

http://www.neb.com/nebecomm/career.asp

If interested, please email your C.V. and statement of interest to:

resumes at neb.com
Attn: Job Code 1102SK

Cheers.

-sanjay

======================
Sanjay Kumar, PhD
Research Scientist
New England Biolabs

=================================================================
Bioinformatics Software Developer

Summary:

Bioinformatics software developer that will work under the direction of a
principle investigator and collaborate with other scientists in designing,
developing, testing and maintaining computational tools, web services, and
potentially large relational databases to support the study of diverse
research topics in molecular biology relevant to New England Biolabs. At
minimum, a BS degree in computer science, biology, physics, or related field
plus 2 years experience as a software developer is required. Proven ability
to design and implement projects using RDBMS software and web-based user
interfaces is essential.


Primary Responsibilities:

  Accurately evaluate proposed projects in terms of their feasibility,
required resources, and estimated timelines and milestones, and effectively
communicate the results to the principle investigator.

  Design, implement, test, deploy, and maintain relational databases
containing molecular biology/genomic data. Translate user requirements into
a database schema.

  Design, implement, test, deploy, and maintain software tools for
querying/browsing/updating data in relational databases, with emphasis on
web accessible applications.

  Design, implement, test, deploy, and maintain software tools to access
external data sources, e.g., at NCBI, EBI, and WormBase, with emphasis on
web accessible applications.

  Assemble bioinformatics pipelines with custom and/or third-party software.

  Provide technical support to end users when necessary.

Technical Expertise:

  Expertise in at least one of the following languages: Java, Perl, Python,
C++, or C is required.

  Experience writing SQL (including DDL) preferably for Apache Derby,
PostgreSQL, Sybase, or MS SQLServer is required.

  Web programming experience using HTML, Javascript, and PHP, and
familiarity with Apache/Tomcat, Glassfish, or Sun Web Server is preferred.

  Experience with object relational mapping frameworks (Hibernate, JDO) and
middleware (J2EE/EJB, Spring) is preferred.

  Experience with SOAP web services is preferred.

  Familiarity with Mac OS, Windows and UNIX and the ability to move easily
between them is beneficial.



If interested, please email your C.V. and statement of interest to:

resumes at neb.com
Attn: Job Code 1102SK


From crackeur at comcast.net  Sat Feb 24 23:28:32 2007
From: crackeur at comcast.net (Jimmy Zhang)
Date: Sat, 24 Feb 2007 20:28:32 -0800
Subject: [Biojava-l] [ANN]VTD-XML 2.0
References: <1133171676.2994.75.camel@zidane>
Message-ID: <015e01c75895$86e20800$0d02a8c0@ximpleware>

 The VTD-XML project team is proud to announce the release of 
version 2.0 of VTD-XML, the next generation XML parser/indexer.
The new features introduced in this version are:

* VTD+XML version 1.0: the world's first true native XML index 
that is simple, general-purpose and back-compatible with XML. 
* NodeRecorder Class that saves VTDNav's cursor location for 
later sequential access.
* Overwrite capability
* Lexically comparisons between VTD and strings

 To download the software, please go to 
http://sourceforge.net/project/showfiles.php?group_id=110612

 To read the latest benchmark report please go to
http://vtd-xml.sf.net/benchmark1.html

 To get the latest API overview
http://www.ximpleware.com/vtd-xml_intro.pdf


From ilhami.visne at gmail.com  Tue Feb 27 09:47:38 2007
From: ilhami.visne at gmail.com (Ilhami Visne)
Date: Tue, 27 Feb 2007 15:47:38 +0100
Subject: [Biojava-l] case-sensitive sequences
Message-ID: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>

my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
using now RichSequenceIterator to iterate over the sequences.

How can i tell biojava that it should parse it case-sensitive? if i call
seq.seqString() method, it should return exactly like it was in the file
with upper- and lower-case.

thanx.

From ilhami.visne at gmail.com  Tue Feb 27 12:54:13 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Tue, 27 Feb 2007 18:54:13 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E44B6F.9090202@ebi.ac.uk>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk>
Message-ID: <45E47045.5010400@gmail.com>

Thank you for quick answer. Here is the part of my code:

BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
RichSequence rs = iter.nextRichSequence();

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> DNA is not case-sensitive. What I suspect you are parsing is the output
> of some sequencing software which is using case as a rough indicator of
> base calling quality?
>
> The case will have been lost when the file was parsed, not at the moment
> you iterate over the resulting sequences. This means that you have to
> modify your file parsing method to become case-sensitive.
>
> The default DNA alphabet is not case-sensitive. It makes no distinction
> between the two, and will convert everything to one case.
>
> If you need to preserve case, you will need to use a custom alphabet
> which treats the cases differently, and also specify a tokenizer which
> is case-sensitive. See the help pages at http://biojava.org/ for help on
> creating new alphabets. Or, have a look at the ABITools.QUALITY alphabet
> in BioJava, which interprets the case and stores the quality scores
> separately.
>
> Note however that your custom alphabet is NOT the same as the original
> DNA alphabet, and so you may not be able to use it in all the standard
> transforms (RNA etc.). If you do want to use these then you will have to
> make a second copy of each sequence using the normal DNA alphabet and
> pass that copy to the routines.
>
> If you post to this list the code you are using to read the file, then I
> can show you where to insert the reference to this new alphabet.
>
> cheers,
> Richard
>
> Ilhami Visne wrote:
>   
>> my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
>> using now RichSequenceIterator to iterate over the sequences.
>>
>> How can i tell biojava that it should parse it case-sensitive? if i call
>> seq.seqString() method, it should return exactly like it was in the file
>> with upper- and lower-case.
>>
>> thanx.
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>     
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> uZKlrdE8y6vMfKcOlm9yBZA=
> =2VZC
> -----END PGP SIGNATURE-----
>
>   


From markjschreiber at gmail.com  Tue Feb 27 21:54:57 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 28 Feb 2007 10:54:57 +0800
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E47045.5010400@gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
Message-ID: <93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>

Hi -

There are also the classes: SoftMaskedAlphabet and
SoftMaskedAlphabet.CaseSensitiveTokenization and
SoftMaskedAlphabet.MaskingDetector. Together these classes let you
read a sequence that contains case sensitive information and (if you
wish) make use of that information. You can also write out the
sequence in the original case sensitive format.

It was originally designed for reading data that had been 'softmasked'
for low complexity regions (eg lower case regions are low complexity
and would be ignored in subsequent analysis) but it would be used for
quality or any other distinction.

- Mark

On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> Thank you for quick answer. Here is the part of my code:
>
> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> RichSequence rs = iter.nextRichSequence();
>
> Richard Holland wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > DNA is not case-sensitive. What I suspect you are parsing is the output
> > of some sequencing software which is using case as a rough indicator of
> > base calling quality?
> >
> > The case will have been lost when the file was parsed, not at the moment
> > you iterate over the resulting sequences. This means that you have to
> > modify your file parsing method to become case-sensitive.
> >
> > The default DNA alphabet is not case-sensitive. It makes no distinction
> > between the two, and will convert everything to one case.
> >
> > If you need to preserve case, you will need to use a custom alphabet
> > which treats the cases differently, and also specify a tokenizer which
> > is case-sensitive. See the help pages at http://biojava.org/ for help on
> > creating new alphabets. Or, have a look at the ABITools.QUALITY alphabet
> > in BioJava, which interprets the case and stores the quality scores
> > separately.
> >
> > Note however that your custom alphabet is NOT the same as the original
> > DNA alphabet, and so you may not be able to use it in all the standard
> > transforms (RNA etc.). If you do want to use these then you will have to
> > make a second copy of each sequence using the normal DNA alphabet and
> > pass that copy to the routines.
> >
> > If you post to this list the code you are using to read the file, then I
> > can show you where to insert the reference to this new alphabet.
> >
> > cheers,
> > Richard
> >
> > Ilhami Visne wrote:
> >
> >> my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
> >> using now RichSequenceIterator to iterate over the sequences.
> >>
> >> How can i tell biojava that it should parse it case-sensitive? if i call
> >> seq.seqString() method, it should return exactly like it was in the file
> >> with upper- and lower-case.
> >>
> >> thanx.
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >>
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >
> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> > uZKlrdE8y6vMfKcOlm9yBZA=
> > =2VZC
> > -----END PGP SIGNATURE-----
> >
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From ilhami.visne at gmail.com  Wed Feb 28 00:15:53 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Wed, 28 Feb 2007 06:15:53 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>	
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
Message-ID: <45E51009.2090605@gmail.com>

Thank you. it does now. i should able to find it myself, but i am really 
not a bioinformaticians yet.

my code (maybe there is someone, who has the same problem like me)

BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
           
Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
SymbolTokenization dnaParser = dna.getTokenization("token");
           
RichSequenceIterator iter = 
RichSequence.IOTools.readFasta(br,dnaParser,null);
RichSequence rs = iter.nextRichSequence();

Mark Schreiber wrote:
> Hi -
>
> There are also the classes: SoftMaskedAlphabet and
> SoftMaskedAlphabet.CaseSensitiveTokenization and
> SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> read a sequence that contains case sensitive information and (if you
> wish) make use of that information. You can also write out the
> sequence in the original case sensitive format.
>
> It was originally designed for reading data that had been 'softmasked'
> for low complexity regions (eg lower case regions are low complexity
> and would be ignored in subsequent analysis) but it would be used for
> quality or any other distinction.
>
> - Mark
>
> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> Thank you for quick answer. Here is the part of my code:
>>
>> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
>> RichSequence rs = iter.nextRichSequence();
>>
>> Richard Holland wrote:
>> > -----BEGIN PGP SIGNED MESSAGE-----
>> > Hash: SHA1
>> >
>> > DNA is not case-sensitive. What I suspect you are parsing is the 
>> output
>> > of some sequencing software which is using case as a rough 
>> indicator of
>> > base calling quality?
>> >
>> > The case will have been lost when the file was parsed, not at the 
>> moment
>> > you iterate over the resulting sequences. This means that you have to
>> > modify your file parsing method to become case-sensitive.
>> >
>> > The default DNA alphabet is not case-sensitive. It makes no 
>> distinction
>> > between the two, and will convert everything to one case.
>> >
>> > If you need to preserve case, you will need to use a custom alphabet
>> > which treats the cases differently, and also specify a tokenizer which
>> > is case-sensitive. See the help pages at http://biojava.org/ for 
>> help on
>> > creating new alphabets. Or, have a look at the ABITools.QUALITY 
>> alphabet
>> > in BioJava, which interprets the case and stores the quality scores
>> > separately.
>> >
>> > Note however that your custom alphabet is NOT the same as the original
>> > DNA alphabet, and so you may not be able to use it in all the standard
>> > transforms (RNA etc.). If you do want to use these then you will 
>> have to
>> > make a second copy of each sequence using the normal DNA alphabet and
>> > pass that copy to the routines.
>> >
>> > If you post to this list the code you are using to read the file, 
>> then I
>> > can show you where to insert the reference to this new alphabet.
>> >
>> > cheers,
>> > Richard
>> >
>> > Ilhami Visne wrote:
>> >
>> >> my sequence files contain case-sensitive symbols (TAATAACgagagg) 
>> and i am
>> >> using now RichSequenceIterator to iterate over the sequences.
>> >>
>> >> How can i tell biojava that it should parse it case-sensitive? if 
>> i call
>> >> seq.seqString() method, it should return exactly like it was in 
>> the file
>> >> with upper- and lower-case.
>> >>
>> >> thanx.
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >>
>> >>
>> > -----BEGIN PGP SIGNATURE-----
>> > Version: GnuPG v1.4.2.2 (GNU/Linux)
>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>> >
>> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
>> > uZKlrdE8y6vMfKcOlm9yBZA=
>> > =2VZC
>> > -----END PGP SIGNATURE-----
>> >
>> >
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>


From ilhami.visne at gmail.com  Wed Feb 28 02:48:46 2007
From: ilhami.visne at gmail.com (Ilhami Visne)
Date: Wed, 28 Feb 2007 08:48:46 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E51009.2090605@gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
	<45E51009.2090605@gmail.com>
Message-ID: <ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>

i've changed my code and called the RestrictionSiteFinder with the new
sequence. it's throwed this exception.

Exception in thread "Thread-25"
java.lang.UnsupportedOperationException: Ambiguity should be handled
at the level of the wrapped Alphabet
        at org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
        at org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
        at org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
        at org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
        at org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)

i understand why it didn't work (lower case symbol 'a' and upper
symbol 'A'), but i can't find a solution. Any idea?

On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> Thank you. it does now. i should able to find it myself, but i am really
> not a bioinformaticians yet.
>
> my code (maybe there is someone, who has the same problem like me)
>
> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>
> Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
> SymbolTokenization dnaParser = dna.getTokenization("token");
>
> RichSequenceIterator iter =
> RichSequence.IOTools.readFasta(br,dnaParser,null);
> RichSequence rs = iter.nextRichSequence();
>
> Mark Schreiber wrote:
> > Hi -
> >
> > There are also the classes: SoftMaskedAlphabet and
> > SoftMaskedAlphabet.CaseSensitiveTokenization and
> > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> > read a sequence that contains case sensitive information and (if you
> > wish) make use of that information. You can also write out the
> > sequence in the original case sensitive format.
> >
> > It was originally designed for reading data that had been 'softmasked'
> > for low complexity regions (eg lower case regions are low complexity
> > and would be ignored in subsequent analysis) but it would be used for
> > quality or any other distinction.
> >
> > - Mark
> >
> > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> >> Thank you for quick answer. Here is the part of my code:
> >>
> >> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> >> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> >> RichSequence rs = iter.nextRichSequence();
> >>
> >> Richard Holland wrote:
> >> > -----BEGIN PGP SIGNED MESSAGE-----
> >> > Hash: SHA1
> >> >
> >> > DNA is not case-sensitive. What I suspect you are parsing is the
> >> output
> >> > of some sequencing software which is using case as a rough
> >> indicator of
> >> > base calling quality?
> >> >
> >> > The case will have been lost when the file was parsed, not at the
> >> moment
> >> > you iterate over the resulting sequences. This means that you have to
> >> > modify your file parsing method to become case-sensitive.
> >> >
> >> > The default DNA alphabet is not case-sensitive. It makes no
> >> distinction
> >> > between the two, and will convert everything to one case.
> >> >
> >> > If you need to preserve case, you will need to use a custom alphabet
> >> > which treats the cases differently, and also specify a tokenizer which
> >> > is case-sensitive. See the help pages at http://biojava.org/ for
> >> help on
> >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
> >> alphabet
> >> > in BioJava, which interprets the case and stores the quality scores
> >> > separately.
> >> >
> >> > Note however that your custom alphabet is NOT the same as the original
> >> > DNA alphabet, and so you may not be able to use it in all the standard
> >> > transforms (RNA etc.). If you do want to use these then you will
> >> have to
> >> > make a second copy of each sequence using the normal DNA alphabet and
> >> > pass that copy to the routines.
> >> >
> >> > If you post to this list the code you are using to read the file,
> >> then I
> >> > can show you where to insert the reference to this new alphabet.
> >> >
> >> > cheers,
> >> > Richard
> >> >
> >> > Ilhami Visne wrote:
> >> >
> >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
> >> and i am
> >> >> using now RichSequenceIterator to iterate over the sequences.
> >> >>
> >> >> How can i tell biojava that it should parse it case-sensitive? if
> >> i call
> >> >> seq.seqString() method, it should return exactly like it was in
> >> the file
> >> >> with upper- and lower-case.
> >> >>
> >> >> thanx.
> >> >> _______________________________________________
> >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >>
> >> >>
> >> > -----BEGIN PGP SIGNATURE-----
> >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >> >
> >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> >> > uZKlrdE8y6vMfKcOlm9yBZA=
> >> > =2VZC
> >> > -----END PGP SIGNATURE-----
> >> >
> >> >
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
>

From markjschreiber at gmail.com  Wed Feb 28 06:03:24 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 28 Feb 2007 19:03:24 +0800
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
	<45E51009.2090605@gmail.com>
	<ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
Message-ID: <93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>

Hi -

Is there any reason why you need to be running the restriction finder
over the soft masked sequence?

Can you post some example code to replicate the bug/annoyance?

If you think this is a genuine bug then please submit a biojava bug
report to http://bugzilla.open-bio.org/
Please also include the example code that demonstrates the bug.

Thanks.

- Mark

On 2/28/07, Ilhami Visne <ilhami.visne at gmail.com> wrote:
> i've changed my code and called the RestrictionSiteFinder with the new
> sequence. it's throwed this exception.
>
> Exception in thread "Thread-25"
> java.lang.UnsupportedOperationException: Ambiguity should be handled
> at the level of the wrapped Alphabet
>         at org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
>         at org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
>         at org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
>         at org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
>         at org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
>
> i understand why it didn't work (lower case symbol 'a' and upper
> symbol 'A'), but i can't find a solution. Any idea?
>
> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> > Thank you. it does now. i should able to find it myself, but i am really
> > not a bioinformaticians yet.
> >
> > my code (maybe there is someone, who has the same problem like me)
> >
> > BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> >
> > Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
> > SymbolTokenization dnaParser = dna.getTokenization("token");
> >
> > RichSequenceIterator iter =
> > RichSequence.IOTools.readFasta(br,dnaParser,null);
> > RichSequence rs = iter.nextRichSequence();
> >
> > Mark Schreiber wrote:
> > > Hi -
> > >
> > > There are also the classes: SoftMaskedAlphabet and
> > > SoftMaskedAlphabet.CaseSensitiveTokenization and
> > > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> > > read a sequence that contains case sensitive information and (if you
> > > wish) make use of that information. You can also write out the
> > > sequence in the original case sensitive format.
> > >
> > > It was originally designed for reading data that had been 'softmasked'
> > > for low complexity regions (eg lower case regions are low complexity
> > > and would be ignored in subsequent analysis) but it would be used for
> > > quality or any other distinction.
> > >
> > > - Mark
> > >
> > > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> > >> Thank you for quick answer. Here is the part of my code:
> > >>
> > >> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> > >> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> > >> RichSequence rs = iter.nextRichSequence();
> > >>
> > >> Richard Holland wrote:
> > >> > -----BEGIN PGP SIGNED MESSAGE-----
> > >> > Hash: SHA1
> > >> >
> > >> > DNA is not case-sensitive. What I suspect you are parsing is the
> > >> output
> > >> > of some sequencing software which is using case as a rough
> > >> indicator of
> > >> > base calling quality?
> > >> >
> > >> > The case will have been lost when the file was parsed, not at the
> > >> moment
> > >> > you iterate over the resulting sequences. This means that you have to
> > >> > modify your file parsing method to become case-sensitive.
> > >> >
> > >> > The default DNA alphabet is not case-sensitive. It makes no
> > >> distinction
> > >> > between the two, and will convert everything to one case.
> > >> >
> > >> > If you need to preserve case, you will need to use a custom alphabet
> > >> > which treats the cases differently, and also specify a tokenizer which
> > >> > is case-sensitive. See the help pages at http://biojava.org/ for
> > >> help on
> > >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
> > >> alphabet
> > >> > in BioJava, which interprets the case and stores the quality scores
> > >> > separately.
> > >> >
> > >> > Note however that your custom alphabet is NOT the same as the original
> > >> > DNA alphabet, and so you may not be able to use it in all the standard
> > >> > transforms (RNA etc.). If you do want to use these then you will
> > >> have to
> > >> > make a second copy of each sequence using the normal DNA alphabet and
> > >> > pass that copy to the routines.
> > >> >
> > >> > If you post to this list the code you are using to read the file,
> > >> then I
> > >> > can show you where to insert the reference to this new alphabet.
> > >> >
> > >> > cheers,
> > >> > Richard
> > >> >
> > >> > Ilhami Visne wrote:
> > >> >
> > >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
> > >> and i am
> > >> >> using now RichSequenceIterator to iterate over the sequences.
> > >> >>
> > >> >> How can i tell biojava that it should parse it case-sensitive? if
> > >> i call
> > >> >> seq.seqString() method, it should return exactly like it was in
> > >> the file
> > >> >> with upper- and lower-case.
> > >> >>
> > >> >> thanx.
> > >> >> _______________________________________________
> > >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >> >>
> > >> >>
> > >> > -----BEGIN PGP SIGNATURE-----
> > >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> > >> >
> > >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> > >> > uZKlrdE8y6vMfKcOlm9yBZA=
> > >> > =2VZC
> > >> > -----END PGP SIGNATURE-----
> > >> >
> > >> >
> > >>
> > >> _______________________________________________
> > >> 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 alainfa at bluewin.ch  Wed Feb 28 08:54:17 2007
From: alainfa at bluewin.ch (Alain Favre)
Date: Wed, 28 Feb 2007 14:54:17 +0100
Subject: [Biojava-l] biojava.utils.bytecode
Message-ID: <000601c75b3f$f1409fc0$2101a8c0@camillealain>

Hello,
Looking for this package whwre can I find it
Thanks for your answer
A. Favre

From ilhami.visne at gmail.com  Wed Feb 28 14:56:36 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Wed, 28 Feb 2007 20:56:36 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>	
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>	
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>	
	<45E51009.2090605@gmail.com>	
	<ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
	<93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>
Message-ID: <45E5DE74.8040008@gmail.com>

Yes, there is one.

i am writing a small program, which my coworker will use. first it 
downloads some repeat masked sequences and then with 
restrictionsitefinder it finds cuts and then exports all fragments.  
these fragments should be repeat masked (case-sensitive) too. after i 
find the cut positions, with SequenceTools.subSequence() i'll extract 
the fragments and write them out.

here is the code sample:

BufferedReader br = new BufferedReader(new FileReader("aSeq.fasta"));
           
Alphabet maskeddna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
SymbolTokenization dnaParser = maskeddna.getTokenization("token");
           
RichSequenceIterator iter = 
RichSequence.IOTools.readFasta(br,dnaParser,null);
RichSequence seq = iter.nextRichSequence();
           
SimpleThreadPool threadPool = new SimpleThreadPool();
RestrictionEnzyme enzyme = RestrictionEnzymeManager.getEnzyme("MseI");
RestrictionMapper mapper = new RestrictionMapper(threadPool);

mapper.addEnzyme(enzyme);
mapper.annotate(seq);

this throws:

Exception in thread "Thread-3" java.lang.UnsupportedOperationException: 
Ambiguity should be handled at the level of the wrapped Alphabet
        at 
org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
        at 
org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
        at 
org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
        at 
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)


Mark Schreiber wrote:
> Hi -
>
> Is there any reason why you need to be running the restriction finder
> over the soft masked sequence?
>
> Can you post some example code to replicate the bug/annoyance?
>
> If you think this is a genuine bug then please submit a biojava bug
> report to http://bugzilla.open-bio.org/
> Please also include the example code that demonstrates the bug.
>
> Thanks.
>
> - Mark
>
> On 2/28/07, Ilhami Visne <ilhami.visne at gmail.com> wrote:
>> i've changed my code and called the RestrictionSiteFinder with the new
>> sequence. it's throwed this exception.
>>
>> Exception in thread "Thread-25"
>> java.lang.UnsupportedOperationException: Ambiguity should be handled
>> at the level of the wrapped Alphabet
>>         at 
>> org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183) 
>>
>>         at 
>> org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223) 
>>
>>         at 
>> org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75) 
>>
>>         at 
>> org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73) 
>>
>>         at 
>> org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295) 
>>
>>
>> i understand why it didn't work (lower case symbol 'a' and upper
>> symbol 'A'), but i can't find a solution. Any idea?
>>
>> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> > Thank you. it does now. i should able to find it myself, but i am 
>> really
>> > not a bioinformaticians yet.
>> >
>> > my code (maybe there is someone, who has the same problem like me)
>> >
>> > BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>> >
>> > Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
>> > SymbolTokenization dnaParser = dna.getTokenization("token");
>> >
>> > RichSequenceIterator iter =
>> > RichSequence.IOTools.readFasta(br,dnaParser,null);
>> > RichSequence rs = iter.nextRichSequence();
>> >
>> > Mark Schreiber wrote:
>> > > Hi -
>> > >
>> > > There are also the classes: SoftMaskedAlphabet and
>> > > SoftMaskedAlphabet.CaseSensitiveTokenization and
>> > > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
>> > > read a sequence that contains case sensitive information and (if you
>> > > wish) make use of that information. You can also write out the
>> > > sequence in the original case sensitive format.
>> > >
>> > > It was originally designed for reading data that had been 
>> 'softmasked'
>> > > for low complexity regions (eg lower case regions are low complexity
>> > > and would be ignored in subsequent analysis) but it would be used 
>> for
>> > > quality or any other distinction.
>> > >
>> > > - Mark
>> > >
>> > > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> > >> Thank you for quick answer. Here is the part of my code:
>> > >>
>> > >> BufferedReader br = new BufferedReader(new 
>> FileReader("seq.fasta"));
>> > >> RichSequenceIterator iter = 
>> RichSequence.IOTools.readFastaDNA(br,null);
>> > >> RichSequence rs = iter.nextRichSequence();
>> > >>
>> > >> Richard Holland wrote:
>> > >> > -----BEGIN PGP SIGNED MESSAGE-----
>> > >> > Hash: SHA1
>> > >> >
>> > >> > DNA is not case-sensitive. What I suspect you are parsing is the
>> > >> output
>> > >> > of some sequencing software which is using case as a rough
>> > >> indicator of
>> > >> > base calling quality?
>> > >> >
>> > >> > The case will have been lost when the file was parsed, not at the
>> > >> moment
>> > >> > you iterate over the resulting sequences. This means that you 
>> have to
>> > >> > modify your file parsing method to become case-sensitive.
>> > >> >
>> > >> > The default DNA alphabet is not case-sensitive. It makes no
>> > >> distinction
>> > >> > between the two, and will convert everything to one case.
>> > >> >
>> > >> > If you need to preserve case, you will need to use a custom 
>> alphabet
>> > >> > which treats the cases differently, and also specify a 
>> tokenizer which
>> > >> > is case-sensitive. See the help pages at http://biojava.org/ for
>> > >> help on
>> > >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
>> > >> alphabet
>> > >> > in BioJava, which interprets the case and stores the quality 
>> scores
>> > >> > separately.
>> > >> >
>> > >> > Note however that your custom alphabet is NOT the same as the 
>> original
>> > >> > DNA alphabet, and so you may not be able to use it in all the 
>> standard
>> > >> > transforms (RNA etc.). If you do want to use these then you will
>> > >> have to
>> > >> > make a second copy of each sequence using the normal DNA 
>> alphabet and
>> > >> > pass that copy to the routines.
>> > >> >
>> > >> > If you post to this list the code you are using to read the file,
>> > >> then I
>> > >> > can show you where to insert the reference to this new alphabet.
>> > >> >
>> > >> > cheers,
>> > >> > Richard
>> > >> >
>> > >> > Ilhami Visne wrote:
>> > >> >
>> > >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
>> > >> and i am
>> > >> >> using now RichSequenceIterator to iterate over the sequences.
>> > >> >>
>> > >> >> How can i tell biojava that it should parse it 
>> case-sensitive? if
>> > >> i call
>> > >> >> seq.seqString() method, it should return exactly like it was in
>> > >> the file
>> > >> >> with upper- and lower-case.
>> > >> >>
>> > >> >> thanx.
>> > >> >> _______________________________________________
>> > >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> > >> >>
>> > >> >>
>> > >> > -----BEGIN PGP SIGNATURE-----
>> > >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
>> > >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>> > >> >
>> > >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
>> > >> > uZKlrdE8y6vMfKcOlm9yBZA=
>> > >> > =2VZC
>> > >> > -----END PGP SIGNATURE-----
>> > >> >
>> > >> >
>> > >>
>> > >> _______________________________________________
>> > >> 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 markjschreiber at gmail.com  Wed Feb 28 20:32:29 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Thu, 1 Mar 2007 09:32:29 +0800
Subject: [Biojava-l] biojava.utils.bytecode
In-Reply-To: <000601c75b3f$f1409fc0$2101a8c0@camillealain>
References: <000601c75b3f$f1409fc0$2101a8c0@camillealain>
Message-ID: <93b45ca50702281732g59b9e8c4k652f58f98c49f225@mail.gmail.com>

Hi -

You need to download the bytecode.jar which can be found at:

http://biojava.org/wiki/BioJava:Download.

- Mark

On 2/28/07, Alain Favre <alainfa at bluewin.ch> wrote:
> Hello,
> Looking for this package whwre can I find it
> Thanks for your answer
> A. Favre
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

From salmantahir1 at gmail.com  Tue Feb  6 11:21:41 2007
From: salmantahir1 at gmail.com (Salman Tahir)
Date: Tue, 6 Feb 2007 11:21:41 +0000
Subject: [Biojava-l] Variable modifications to Protein sequences
Message-ID: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>

Hi,

I am emailing regarding a java program that I am writing which deals with
the in silico manipulation of cross-linked peptides.

I would like to manipulate protein sequences by taking into account variable
modifications using BioJava classes (if possible). For example:

If I have the following variable modification:
hydroxo-BS2GD4 (N-term, K): 118.0563805

And the following sequence: FLEKQNKER (assuming it contains the N-term)

I need to generate the following sequences
FLEKQNKER -> FLEKQNKER, FLEKhydroxo-BS2GD0QNKER, FLEKQNKhydroxo-BS2GD0ER,
FLEKhydroxo-BS2GD0QNKhydroxo-BS2GD0 ER, Fhydroxo-BS2GD0LEK QNKER and so on -
generating a total of 8 peptide sequences with different masses.

Is there a way i can generate these additional sequences using BioJava? Any
help would be mostly appreciated.

- Salman


From markjschreiber at gmail.com  Wed Feb  7 15:30:47 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 7 Feb 2007 23:30:47 +0800
Subject: [Biojava-l] Variable modifications to Protein sequences
In-Reply-To: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>
References: <2049e51a0702060321l349cd04dp6828b30e3ff980b@mail.gmail.com>
Message-ID: <93b45ca50702070730n79d0aea2seefa3f3af5cebd1@mail.gmail.com>

Hi -
I think that the best approach would be to define your own custom
alphabet (possibly with a custom tokenization). You could then create
SymbolLists or sequences with this new alphabet.
- Mark

On 2/6/07, Salman Tahir <salmantahir1 at gmail.com> wrote:
> Hi,
>
> I am emailing regarding a java program that I am writing which deals with
> the in silico manipulation of cross-linked peptides.
>
> I would like to manipulate protein sequences by taking into account variable
> modifications using BioJava classes (if possible). For example:
>
> If I have the following variable modification:
> hydroxo-BS2GD4 (N-term, K): 118.0563805
>
> And the following sequence: FLEKQNKER (assuming it contains the N-term)
>
> I need to generate the following sequences
> FLEKQNKER -> FLEKQNKER, FLEKhydroxo-BS2GD0QNKER, FLEKQNKhydroxo-BS2GD0ER,
> FLEKhydroxo-BS2GD0QNKhydroxo-BS2GD0 ER, Fhydroxo-BS2GD0LEK QNKER and so on -
> generating a total of 8 peptide sequences with different masses.
>
> Is there a way i can generate these additional sequences using BioJava? Any
> help would be mostly appreciated.
>
> - Salman
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From su24 at st-andrews.ac.uk  Wed Feb  7 16:11:37 2007
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Wed,  7 Feb 2007 16:11:37 +0000
Subject: [Biojava-l] Use Of Blosum62
Message-ID: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>


Dear All,

I am having a problem using the Blosum62 matrix file from the NCBI website for
use in Smith-Waterman alignments. When I attempt to run my code reading in the
file to initialise the Substitution Matrix Object the following exception is
thrown

"org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
contain character: '*'"



Thanking you in advance,

Saif



--------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Sir Harold Mitchell Building
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk



From su24 at st-andrews.ac.uk  Wed Feb  7 16:38:52 2007
From: su24 at st-andrews.ac.uk (Saif Ur-Rehman)
Date: Wed,  7 Feb 2007 16:38:52 +0000
Subject: [Biojava-l] Use Of Blosum62
In-Reply-To: <45C9FD73.5040200@ebi.ac.uk>
References: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>
	<45C9FD73.5040200@ebi.ac.uk>
Message-ID: <1170866332.45ca009c26757@webmail.st-andrews.ac.uk>

Hi,

Here is the code I am using


Cheers,

Saif

public static void main(String args[])
	{
		String x=("prot sequence excluded");
		String y=("prot sequence excluded");

		try {

	      FiniteAlphabet alphabet
(FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");

SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet, new
File("///Users/su24/BLOSUM62"));

// The above line causes the exception

	      SequenceAlignment  aligner = new SmithWaterman( -1,3,2,2,1,matrix);
	      Sequence query  = ProteinTools.createProteinSequence(x, "query");
	      Sequence target = ProteinTools.createProteinSequence(y, "target");
	      aligner.pairwiseAlignment(query, target);


	      System.out.println("\nlocal alignment with SmithWaterman:\n" +
aligner.getAlignmentString());
	    }

	catch (Exception exc) {
	      exc.printStackTrace();
	    }
	  }


	}

Quoting Richard Holland <holland at ebi.ac.uk>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi. You need to include your complete program code in your email so that
> we can accurately diagnose the problem.
>
> cheers,
> Richard
>
> Saif Ur-Rehman wrote:
> > Dear All,
> >
> > I am having a problem using the Blosum62 matrix file from the NCBI website
> for
> > use in Smith-Waterman alignments. When I attempt to run my code reading in
> the
> > file to initialise the Substitution Matrix Object the following exception
> is
> > thrown
> >
> > "org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
> > contain character: '*'"
> >
> >
> >
> > Thanking you in advance,
> >
> > Saif
> >
> >
> >
> >
>
--------------------------------------------------------------------------------
> > Saif Ur-Rehman
> > Research Student
> > The Centre for Evolution, Genes & Genomics (CEGG)
> > Sir Harold Mitchell Building
> > School of Biology
> > The University of St Andrews
> > St Andrews,
> > Fife
> > Scotland,UK
> >
> > ------------------------------------------------------------------
> > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFFyf1y4C5LeMEKA/QRAp7zAJ9ncsgYyBBRDrgSBnANTYv0xYI+PwCgpGv0
> cQQ8vFVB8QtKW9kAt9pRSEQ=
> =2rLL
> -----END PGP SIGNATURE-----
>


-------------------------------------------------------------------------------
Saif Ur-Rehman
Research Student
The Centre for Evolution, Genes & Genomics (CEGG)
Sir Harold Mitchell Building
School of Biology
The University of St Andrews
St Andrews,
Fife
Scotland,UK

------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk



From andreas.draeger at uni-tuebingen.de  Wed Feb  7 18:15:59 2007
From: andreas.draeger at uni-tuebingen.de (=?ISO-8859-1?Q?Andreas_Dr=E4ger?=)
Date: Wed, 07 Feb 2007 19:15:59 +0100
Subject: [Biojava-l] Use Of Blosum62
In-Reply-To: <1170866332.45ca009c26757@webmail.st-andrews.ac.uk>
References: <1170864697.45c9fa39303a5@webmail.st-andrews.ac.uk>	<45C9FD73.5040200@ebi.ac.uk>
	<1170866332.45ca009c26757@webmail.st-andrews.ac.uk>
Message-ID: <45CA175F.1050105@uni-tuebingen.de>

Hey Saif,

> 	      FiniteAlphabet alphabet
> (FiniteAlphabetAlphabetManager.alphabetForName("PROTEIN");
> 

This cannot work because the symbol "*" is indeed not included in the 
alphabet "PROTEIN" as it marks the termination symbol. You will need to 
use the alphabet "PROTEIN-TERM".
I hope that helps.
If I remember correctly, there have been discussions about that special 
character in previous e-mails on that list.

Cheers,
Andreas

-- 
Dipl.-Bioinform. Andreas Dr?ger
Eberhard Karls University T?bingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 T?bingen
Germany

Phone: +49-7071-29-70436
Fax:   +49-7071-29-5091


From Russell.Smithies at agresearch.co.nz  Mon Feb 12 00:55:17 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 12 Feb 2007 13:55:17 +1300
Subject: [Biojava-l] New Zealand bioinformatician vacancy
In-Reply-To: <6dce9a0b0702110814v16d50c5dtc1c8c6f21f14c450@mail.gmail.com>
References: <1170950909.6074.30.camel@localhost><6dce9a0b0702081123j3e8efe89r4e2a93b88d4029d9@mail.gmail.com><1170967751.6084.18.camel@localhost><6dce9a0b0702081307s11683737r17e8d22b47ed6fef@mail.gmail.com><1170970046.6084.36.camel@localhost><6dce9a0b0702081552n28e0aa79x79a8d4eb659fe119@mail.gmail.com><1171105304.5853.11.camel@localhost>
	<6dce9a0b0702110814v16d50c5dtc1c8c6f21f14c450@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C04AC32D2@imail.agresearch.co.nz>

Hi all,

I hope you don't mind me posting an advert but we have an opening for a
bioinformatician.

So if you'd like to work in New Zealand, read on...

 

thanx,

Russell

Russell Smithies 
Bioinformatics Software Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

AgResearch Farming Food and Health. First 
Te Ahuwhenua, Te Kai me te Whai Ora. Tuatahi 

Invermay  Research Centre 
Puddle Alley, 
Mosgiel, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  
www.agresearch.co.nz 

 ========================================================== 

 

 

 Bioinformatician

AgResearch - Applied Biotechnologies

 

As part of AgResearch's company strategy we are continuing to grow our
business in the area of bioinformatics.  This capability is essential
for our science discovery.

 

In this position you will be part of a national team of 26
bioinformaticians, mathematical biologists and statisticians and be
based at our Grasslands campus at Palmerston North.  This is a permanent
position.

 

You will be an advocate for bioinformatics within AgResearch; you will
work collaboratively on projects and will provide bioinformatics
training and advice to science staff working in the biotechnology area.

 

We are seeking a person who has:

*               An excellent tertiary qualification in molecular biology
or genetics

*               Experience with the use of bioinformatics applications

*               Knowledge of life sciences databases and the internet

*               Well developed IT technical skills and web based
technologies

*               Experience in a training environment

*               Excellent writing, speaking and interpersonal skills

*               Familiarity with Perl, Java or Unix Scripting

 

If you possess the above skills, we would like to hear from you.

 

To find out more about this position please contact Peter Johnstone by
email peter.johnstone at agresearch.co.nz or alternatively phone +64 3 489
9081.

 

For a job description and to apply on line please go to
http://www.agresearch.co.nz/recruitment .  Vacancy No AGR494.  Please
provide contact details for 2 Referees with your application.

 

For general information on AgResearch please visit our website at
www.agresearch.co.nz <http://www.agresearch.co.nz/> 

 

Applications close 9th March 2007.

 

Linda Murray

Science Administrator

AgResearch Limited

Invermay Agricultural Centre

Private Bag 50034

Mosgiel, New Zealand

Phone: +64 3 489 9011

Email:  linda.murray at agresearch.co.nz 


=======================================================================
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From salmantahir1 at gmail.com  Mon Feb 12 10:41:40 2007
From: salmantahir1 at gmail.com (Salman Tahir)
Date: Mon, 12 Feb 2007 10:41:40 +0000
Subject: [Biojava-l] Tokenization
Message-ID: <2049e51a0702120241k135a92edl235910394f1d124c@mail.gmail.com>

Hi,

I've created a custom alphabet and I would like to use it to parse a file.
After defining the symbols in the alphabet I do the following:

SymbolTokenization parser = alpha.getTokenization("token");

('alpha being the custom alphabet'). However I get the following error:

"BioException: There is no tokenization 'token' defined in alphabet Variable
Modifications"

I understand this to mean that I have to populate the new tokenization
appropriately because this is a new alphabet. However, I cannot find any
examples that show how to achieve this. Can anyone help?

- Salman


From m.titulaer at erasmusmc.nl  Wed Feb 14 15:38:58 2007
From: m.titulaer at erasmusmc.nl (Mark Titulaer)
Date: Wed, 14 Feb 2007 16:38:58 +0100
Subject: [Biojava-l] Conversion Applied Bioisystems MALDI Voyager DE-STR
 .dat file into peak list
Message-ID: <45D32D12.3070800@erasmusmc.nl>

I would like to convert an Applied Biosystems  MALDI Voyager DE-STR  
.dat file into a peak list.
Is there any library available ?






From paolo.romano at istge.it  Tue Feb 20 10:39:30 2007
From: paolo.romano at istge.it (Paolo Romano)
Date: Tue, 20 Feb 2007 11:39:30 +0100
Subject: [Biojava-l] Final Call for Papers NETTAB 2007
Message-ID: <7.0.1.0.0.20070220113922.01e9c968@istge.it>

=================================
Apologies, if you're receiving multiple copies
=================================

Final Call for Papers

7th International Workshop NETTAB 2007
June 12-15, 2006
Department of Computer Science, University of Pisa, Pisa
http://www.nettab.org/2007/

FOCUS THEME
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications

ADJUNCT THEMES
Algorithms in bioinformatics
Formal Methods for Systems Biology
Network Tools and Applications in Bioinformatics

AIMS
This workshop aims at getting together 
biologists, bioinformaticians, computer 
scientists and linguists to try to answer the following questions:
- Is the Semantic Web of some use for Bioinformatics?
- Which goals should have a Semantic Web for Bioinformatics?
- Which standards, technologies and tools of the 
Semantic Web can most profitably be used in Bioinformatics?
- Which application did the Semantic Web already find in Bioinformatics?
- Which current Bioinformatics research problems 
can be solved by the Semantic Web?
- Which are the short, medium and long term 
perspectives in applying Semantic Web technologies to Bionformatics?

The workshop also intends to:
- introduce the basic knowledge of related 
standards and technologies, in a non trivial way 
through invited lectures and tutorials
- outline the promising features of the Semantic 
Web in bioinformatics through invited lectures and open discussion
- show some valuable examples in bioinformatics 
through invited lectures, oral communications and posters
- support as much discussion as possible through 
open discussions and a panel discussion
- practically demonstrate "how it works" through tutorials

INVITED SPEAKERS
We are extremely glad to inform you that four 
excellent speakers have accepted to give an 
invited lecture at next NETTAB workshop.
+ Session on Goals of the Semantic Web in Bioinformatics
    Invited speaker: Eric Neumann, Co-chair of 
the Health Care and Life Science Interest Group 
of the Semantic Web Activity at W3C & Teranode Inc., USA
+ Session on Semantic Web Standards and Technologies
    Invited speaker: Guus Schreiber, Chair of 
Semantic Web Deployment Interest Group at W3C & 
University of Amsterdam, The Netherlands
+ Session on Semantic Web Tools
    Invited speaker: Olivier Bodenreider, Medical 
Ontology Research, National Library of Medicine, USA
+ Session on Applications of Semantic Web in Bioinformatics
    Invited speakers: Michael Schroeder, Biotec 
TU Dresden, Germany, and Albert Burger, Heriot-Watt University, Scotland, UK
Titles of the lectures will soon be announced.

TOPICS
NETTAB workshops also include general sessions on 
Network Tools and Applications in Biology and 
adjunct focus topics selected by local organizers.
You are therefore welcome to submit your work on any of the followings topics:

Goals of a Semantic Web for Bioinformatics:
Standards, Technologies, Tools for the Semantic Web
Systems for a Semantic Web for Bioinformatics:
Existing and perspective applications of the Semantic Web for Bioinformatics

Algorithms in Bioinformatics
Formal Methods for Systems Biology
Network Tools and Applications in Bioinformatics

DEADLINES
Submission of oral communications: March 16, 2007
Proposals for tutorials: March 16, 2007
Submission of posters: April 20, 2007
Early Registration Deadline: April 27, 2007

SUBMISSION OF CONTRIBUTIONS
You are welcome to submit your contributions 
through the MyReview system at the following URL: 
http://www.nettab.org/2007/myreview/ .
This is a two steps submission procedure. You 
will have to submit first an abstract and later the paper.
You are invited to prepare your contribution 
according to instructions available at 
http://www.biomedcentral.com/bmcbioinformatics/ifora/ 
(specially, see "Preparing main manuscript text" section).
See the workshop's web site for more details 
about the preparation of the papers.

PUBLICATION OF PAPERS AND POSTERS
All accepted oral communications and posters will 
be published in the Workshop's Proceedings that 
will be distributed to all participants.
Selected papers will be published by BMC Bioinformatics as a Supplement Issue.
When submitting, you will be asked if your 
submission is intended for the workshop only or 
for the publication in BMC Bioinformatics too.
The papers will be reviewed by the members of the 
Programme Committee. They will decide whether the 
papers are accepted for the workshop only or for 
the publication in BMC Bioinformatics as well.
The workshop will engage itself to pay part of 
the cost of the publication, but please be 
advised that depending on the final budget of the 
workshop you could be requested to contribute to 
publication costs which has been set to 600 British pounds per paper.
For any further information or clarification, 
please contact the organization by email at info at nettab.org .

CHAIRS
P. Romano, Bioinformatics, Natl Cancer Research Inst., Italy
M. Schr?der, Biotechnology Centre, TU Dresden, Germany
N. Cannata, Mathematics & Computer Science Dept, Univ. of Camerino, Italy
O. Signore, ISTI, National Research Council, Italy

PROGRAMME COMMITTEE
G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT
C. Baker, Institute for Infocomm Research (I2R), SG
P. Barahona, Department of Informatics, New University of Lisboa, PT
L. Barrio-Alvers, Transinsight GmbH, DE
O. Bodenreider, National Library of Medicine, USA
A. Burger, Department of Computer Science, Heriot-Watt University, UK
M. Cannataro, Experimental and Clinical Medicine 
Dept, Univ. of Catanzaro "Magna Graecia", IT
W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA
M. Cockerill, BioMed Central, UK
M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR
R. Dieng, INRIA, Sophia Antipolis, FR
L. Grivell, European Molecular Biology Organisation, DE
M. Harris, European Bioinformatics Institute, UK
M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT
C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT
J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK
M. Krallinger, Spanish National Cancer Research Center (CNIO), ES
L. Krippahl, Department of Informatics, New University of Lisboa, PT
P. Lambrix, Computer and Information Science Dept, Link?ping University, SE
U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE
J. Luciano, Department of Genetics, Harvard Medical School, USA
R. Marangoni, Computer Science Department, University of Pisa, IT
M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT
M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT
G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT
E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT
S. Moeller, Institute of Neuro- and Bioinformatics, University of L?beck, DE
S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE
D. Quann, IBM Software Group, USA
D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA
S.-A. Sansone, European Bioinformatics Institute, UK
M. Senger, International Rice Research Institute, PH
D. Turi, School of Computer Science, University of Manchester, UK
G. Vetere, IBM Center for Advanced Studies of Rome, IT
D. Zaccagnini, Language and Computing, USA

Looking forward to seeing you all in Tuscany.

Best regards.

On behalf of the Chairs and of the Organizing Committee

Paolo Romano

Paolo Romano (paolo.romano at istge.it)
Bioinformatics and Structural Proteomics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295




From kumar at neb.com  Wed Feb 21 21:33:48 2007
From: kumar at neb.com (Sanjay Kumar)
Date: Wed, 21 Feb 2007 16:33:48 -0500
Subject: [Biojava-l] Job opportunity - Bioinformatics Software Developer
Message-ID: <C20224EC.2AA1%kumar@neb.com>

Hi-

Sorry for the job posting, but NEB has an opening for a bioinformatics
software developer that might be just right for someone with BioJava
experience. We are located just north of Boston Massachusetts, USA, and the
work environment is wonderful.

The posting is listed below and at our web site:

http://www.neb.com/nebecomm/career.asp

If interested, please email your C.V. and statement of interest to:

resumes at neb.com
Attn: Job Code 1102SK

Cheers.

-sanjay

======================
Sanjay Kumar, PhD
Research Scientist
New England Biolabs

=================================================================
Bioinformatics Software Developer

Summary:

Bioinformatics software developer that will work under the direction of a
principle investigator and collaborate with other scientists in designing,
developing, testing and maintaining computational tools, web services, and
potentially large relational databases to support the study of diverse
research topics in molecular biology relevant to New England Biolabs. At
minimum, a BS degree in computer science, biology, physics, or related field
plus 2 years experience as a software developer is required. Proven ability
to design and implement projects using RDBMS software and web-based user
interfaces is essential.


Primary Responsibilities:

  Accurately evaluate proposed projects in terms of their feasibility,
required resources, and estimated timelines and milestones, and effectively
communicate the results to the principle investigator.

  Design, implement, test, deploy, and maintain relational databases
containing molecular biology/genomic data. Translate user requirements into
a database schema.

  Design, implement, test, deploy, and maintain software tools for
querying/browsing/updating data in relational databases, with emphasis on
web accessible applications.

  Design, implement, test, deploy, and maintain software tools to access
external data sources, e.g., at NCBI, EBI, and WormBase, with emphasis on
web accessible applications.

  Assemble bioinformatics pipelines with custom and/or third-party software.

  Provide technical support to end users when necessary.

Technical Expertise:

  Expertise in at least one of the following languages: Java, Perl, Python,
C++, or C is required.

  Experience writing SQL (including DDL) preferably for Apache Derby,
PostgreSQL, Sybase, or MS SQLServer is required.

  Web programming experience using HTML, Javascript, and PHP, and
familiarity with Apache/Tomcat, Glassfish, or Sun Web Server is preferred.

  Experience with object relational mapping frameworks (Hibernate, JDO) and
middleware (J2EE/EJB, Spring) is preferred.

  Experience with SOAP web services is preferred.

  Familiarity with Mac OS, Windows and UNIX and the ability to move easily
between them is beneficial.



If interested, please email your C.V. and statement of interest to:

resumes at neb.com
Attn: Job Code 1102SK



From crackeur at comcast.net  Sun Feb 25 04:28:32 2007
From: crackeur at comcast.net (Jimmy Zhang)
Date: Sat, 24 Feb 2007 20:28:32 -0800
Subject: [Biojava-l] [ANN]VTD-XML 2.0
References: <1133171676.2994.75.camel@zidane>
Message-ID: <015e01c75895$86e20800$0d02a8c0@ximpleware>

 The VTD-XML project team is proud to announce the release of 
version 2.0 of VTD-XML, the next generation XML parser/indexer.
The new features introduced in this version are:

* VTD+XML version 1.0: the world's first true native XML index 
that is simple, general-purpose and back-compatible with XML. 
* NodeRecorder Class that saves VTDNav's cursor location for 
later sequential access.
* Overwrite capability
* Lexically comparisons between VTD and strings

 To download the software, please go to 
http://sourceforge.net/project/showfiles.php?group_id=110612

 To read the latest benchmark report please go to
http://vtd-xml.sf.net/benchmark1.html

 To get the latest API overview
http://www.ximpleware.com/vtd-xml_intro.pdf



From ilhami.visne at gmail.com  Tue Feb 27 14:47:38 2007
From: ilhami.visne at gmail.com (Ilhami Visne)
Date: Tue, 27 Feb 2007 15:47:38 +0100
Subject: [Biojava-l] case-sensitive sequences
Message-ID: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>

my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
using now RichSequenceIterator to iterate over the sequences.

How can i tell biojava that it should parse it case-sensitive? if i call
seq.seqString() method, it should return exactly like it was in the file
with upper- and lower-case.

thanx.


From ilhami.visne at gmail.com  Tue Feb 27 17:54:13 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Tue, 27 Feb 2007 18:54:13 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E44B6F.9090202@ebi.ac.uk>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk>
Message-ID: <45E47045.5010400@gmail.com>

Thank you for quick answer. Here is the part of my code:

BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
RichSequence rs = iter.nextRichSequence();

Richard Holland wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> DNA is not case-sensitive. What I suspect you are parsing is the output
> of some sequencing software which is using case as a rough indicator of
> base calling quality?
>
> The case will have been lost when the file was parsed, not at the moment
> you iterate over the resulting sequences. This means that you have to
> modify your file parsing method to become case-sensitive.
>
> The default DNA alphabet is not case-sensitive. It makes no distinction
> between the two, and will convert everything to one case.
>
> If you need to preserve case, you will need to use a custom alphabet
> which treats the cases differently, and also specify a tokenizer which
> is case-sensitive. See the help pages at http://biojava.org/ for help on
> creating new alphabets. Or, have a look at the ABITools.QUALITY alphabet
> in BioJava, which interprets the case and stores the quality scores
> separately.
>
> Note however that your custom alphabet is NOT the same as the original
> DNA alphabet, and so you may not be able to use it in all the standard
> transforms (RNA etc.). If you do want to use these then you will have to
> make a second copy of each sequence using the normal DNA alphabet and
> pass that copy to the routines.
>
> If you post to this list the code you are using to read the file, then I
> can show you where to insert the reference to this new alphabet.
>
> cheers,
> Richard
>
> Ilhami Visne wrote:
>   
>> my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
>> using now RichSequenceIterator to iterate over the sequences.
>>
>> How can i tell biojava that it should parse it case-sensitive? if i call
>> seq.seqString() method, it should return exactly like it was in the file
>> with upper- and lower-case.
>>
>> thanx.
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>>     
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.2.2 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> uZKlrdE8y6vMfKcOlm9yBZA=
> =2VZC
> -----END PGP SIGNATURE-----
>
>   



From markjschreiber at gmail.com  Wed Feb 28 02:54:57 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 28 Feb 2007 10:54:57 +0800
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E47045.5010400@gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
Message-ID: <93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>

Hi -

There are also the classes: SoftMaskedAlphabet and
SoftMaskedAlphabet.CaseSensitiveTokenization and
SoftMaskedAlphabet.MaskingDetector. Together these classes let you
read a sequence that contains case sensitive information and (if you
wish) make use of that information. You can also write out the
sequence in the original case sensitive format.

It was originally designed for reading data that had been 'softmasked'
for low complexity regions (eg lower case regions are low complexity
and would be ignored in subsequent analysis) but it would be used for
quality or any other distinction.

- Mark

On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> Thank you for quick answer. Here is the part of my code:
>
> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> RichSequence rs = iter.nextRichSequence();
>
> Richard Holland wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > DNA is not case-sensitive. What I suspect you are parsing is the output
> > of some sequencing software which is using case as a rough indicator of
> > base calling quality?
> >
> > The case will have been lost when the file was parsed, not at the moment
> > you iterate over the resulting sequences. This means that you have to
> > modify your file parsing method to become case-sensitive.
> >
> > The default DNA alphabet is not case-sensitive. It makes no distinction
> > between the two, and will convert everything to one case.
> >
> > If you need to preserve case, you will need to use a custom alphabet
> > which treats the cases differently, and also specify a tokenizer which
> > is case-sensitive. See the help pages at http://biojava.org/ for help on
> > creating new alphabets. Or, have a look at the ABITools.QUALITY alphabet
> > in BioJava, which interprets the case and stores the quality scores
> > separately.
> >
> > Note however that your custom alphabet is NOT the same as the original
> > DNA alphabet, and so you may not be able to use it in all the standard
> > transforms (RNA etc.). If you do want to use these then you will have to
> > make a second copy of each sequence using the normal DNA alphabet and
> > pass that copy to the routines.
> >
> > If you post to this list the code you are using to read the file, then I
> > can show you where to insert the reference to this new alphabet.
> >
> > cheers,
> > Richard
> >
> > Ilhami Visne wrote:
> >
> >> my sequence files contain case-sensitive symbols (TAATAACgagagg) and i am
> >> using now RichSequenceIterator to iterate over the sequences.
> >>
> >> How can i tell biojava that it should parse it case-sensitive? if i call
> >> seq.seqString() method, it should return exactly like it was in the file
> >> with upper- and lower-case.
> >>
> >> thanx.
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >>
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >
> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> > uZKlrdE8y6vMfKcOlm9yBZA=
> > =2VZC
> > -----END PGP SIGNATURE-----
> >
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From ilhami.visne at gmail.com  Wed Feb 28 05:15:53 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Wed, 28 Feb 2007 06:15:53 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>	
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
Message-ID: <45E51009.2090605@gmail.com>

Thank you. it does now. i should able to find it myself, but i am really 
not a bioinformaticians yet.

my code (maybe there is someone, who has the same problem like me)

BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
           
Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
SymbolTokenization dnaParser = dna.getTokenization("token");
           
RichSequenceIterator iter = 
RichSequence.IOTools.readFasta(br,dnaParser,null);
RichSequence rs = iter.nextRichSequence();

Mark Schreiber wrote:
> Hi -
>
> There are also the classes: SoftMaskedAlphabet and
> SoftMaskedAlphabet.CaseSensitiveTokenization and
> SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> read a sequence that contains case sensitive information and (if you
> wish) make use of that information. You can also write out the
> sequence in the original case sensitive format.
>
> It was originally designed for reading data that had been 'softmasked'
> for low complexity regions (eg lower case regions are low complexity
> and would be ignored in subsequent analysis) but it would be used for
> quality or any other distinction.
>
> - Mark
>
> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> Thank you for quick answer. Here is the part of my code:
>>
>> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
>> RichSequence rs = iter.nextRichSequence();
>>
>> Richard Holland wrote:
>> > -----BEGIN PGP SIGNED MESSAGE-----
>> > Hash: SHA1
>> >
>> > DNA is not case-sensitive. What I suspect you are parsing is the 
>> output
>> > of some sequencing software which is using case as a rough 
>> indicator of
>> > base calling quality?
>> >
>> > The case will have been lost when the file was parsed, not at the 
>> moment
>> > you iterate over the resulting sequences. This means that you have to
>> > modify your file parsing method to become case-sensitive.
>> >
>> > The default DNA alphabet is not case-sensitive. It makes no 
>> distinction
>> > between the two, and will convert everything to one case.
>> >
>> > If you need to preserve case, you will need to use a custom alphabet
>> > which treats the cases differently, and also specify a tokenizer which
>> > is case-sensitive. See the help pages at http://biojava.org/ for 
>> help on
>> > creating new alphabets. Or, have a look at the ABITools.QUALITY 
>> alphabet
>> > in BioJava, which interprets the case and stores the quality scores
>> > separately.
>> >
>> > Note however that your custom alphabet is NOT the same as the original
>> > DNA alphabet, and so you may not be able to use it in all the standard
>> > transforms (RNA etc.). If you do want to use these then you will 
>> have to
>> > make a second copy of each sequence using the normal DNA alphabet and
>> > pass that copy to the routines.
>> >
>> > If you post to this list the code you are using to read the file, 
>> then I
>> > can show you where to insert the reference to this new alphabet.
>> >
>> > cheers,
>> > Richard
>> >
>> > Ilhami Visne wrote:
>> >
>> >> my sequence files contain case-sensitive symbols (TAATAACgagagg) 
>> and i am
>> >> using now RichSequenceIterator to iterate over the sequences.
>> >>
>> >> How can i tell biojava that it should parse it case-sensitive? if 
>> i call
>> >> seq.seqString() method, it should return exactly like it was in 
>> the file
>> >> with upper- and lower-case.
>> >>
>> >> thanx.
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >>
>> >>
>> > -----BEGIN PGP SIGNATURE-----
>> > Version: GnuPG v1.4.2.2 (GNU/Linux)
>> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>> >
>> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
>> > uZKlrdE8y6vMfKcOlm9yBZA=
>> > =2VZC
>> > -----END PGP SIGNATURE-----
>> >
>> >
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>



From ilhami.visne at gmail.com  Wed Feb 28 07:48:46 2007
From: ilhami.visne at gmail.com (Ilhami Visne)
Date: Wed, 28 Feb 2007 08:48:46 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <45E51009.2090605@gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
	<45E51009.2090605@gmail.com>
Message-ID: <ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>

i've changed my code and called the RestrictionSiteFinder with the new
sequence. it's throwed this exception.

Exception in thread "Thread-25"
java.lang.UnsupportedOperationException: Ambiguity should be handled
at the level of the wrapped Alphabet
        at org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
        at org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
        at org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
        at org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
        at org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)

i understand why it didn't work (lower case symbol 'a' and upper
symbol 'A'), but i can't find a solution. Any idea?

On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> Thank you. it does now. i should able to find it myself, but i am really
> not a bioinformaticians yet.
>
> my code (maybe there is someone, who has the same problem like me)
>
> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>
> Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
> SymbolTokenization dnaParser = dna.getTokenization("token");
>
> RichSequenceIterator iter =
> RichSequence.IOTools.readFasta(br,dnaParser,null);
> RichSequence rs = iter.nextRichSequence();
>
> Mark Schreiber wrote:
> > Hi -
> >
> > There are also the classes: SoftMaskedAlphabet and
> > SoftMaskedAlphabet.CaseSensitiveTokenization and
> > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> > read a sequence that contains case sensitive information and (if you
> > wish) make use of that information. You can also write out the
> > sequence in the original case sensitive format.
> >
> > It was originally designed for reading data that had been 'softmasked'
> > for low complexity regions (eg lower case regions are low complexity
> > and would be ignored in subsequent analysis) but it would be used for
> > quality or any other distinction.
> >
> > - Mark
> >
> > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> >> Thank you for quick answer. Here is the part of my code:
> >>
> >> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> >> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> >> RichSequence rs = iter.nextRichSequence();
> >>
> >> Richard Holland wrote:
> >> > -----BEGIN PGP SIGNED MESSAGE-----
> >> > Hash: SHA1
> >> >
> >> > DNA is not case-sensitive. What I suspect you are parsing is the
> >> output
> >> > of some sequencing software which is using case as a rough
> >> indicator of
> >> > base calling quality?
> >> >
> >> > The case will have been lost when the file was parsed, not at the
> >> moment
> >> > you iterate over the resulting sequences. This means that you have to
> >> > modify your file parsing method to become case-sensitive.
> >> >
> >> > The default DNA alphabet is not case-sensitive. It makes no
> >> distinction
> >> > between the two, and will convert everything to one case.
> >> >
> >> > If you need to preserve case, you will need to use a custom alphabet
> >> > which treats the cases differently, and also specify a tokenizer which
> >> > is case-sensitive. See the help pages at http://biojava.org/ for
> >> help on
> >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
> >> alphabet
> >> > in BioJava, which interprets the case and stores the quality scores
> >> > separately.
> >> >
> >> > Note however that your custom alphabet is NOT the same as the original
> >> > DNA alphabet, and so you may not be able to use it in all the standard
> >> > transforms (RNA etc.). If you do want to use these then you will
> >> have to
> >> > make a second copy of each sequence using the normal DNA alphabet and
> >> > pass that copy to the routines.
> >> >
> >> > If you post to this list the code you are using to read the file,
> >> then I
> >> > can show you where to insert the reference to this new alphabet.
> >> >
> >> > cheers,
> >> > Richard
> >> >
> >> > Ilhami Visne wrote:
> >> >
> >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
> >> and i am
> >> >> using now RichSequenceIterator to iterate over the sequences.
> >> >>
> >> >> How can i tell biojava that it should parse it case-sensitive? if
> >> i call
> >> >> seq.seqString() method, it should return exactly like it was in
> >> the file
> >> >> with upper- and lower-case.
> >> >>
> >> >> thanx.
> >> >> _______________________________________________
> >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >> >>
> >> >>
> >> > -----BEGIN PGP SIGNATURE-----
> >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> >> >
> >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> >> > uZKlrdE8y6vMfKcOlm9yBZA=
> >> > =2VZC
> >> > -----END PGP SIGNATURE-----
> >> >
> >> >
> >>
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
> >
>
>


From markjschreiber at gmail.com  Wed Feb 28 11:03:24 2007
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Wed, 28 Feb 2007 19:03:24 +0800
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>
	<45E51009.2090605@gmail.com>
	<ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
Message-ID: <93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>

Hi -

Is there any reason why you need to be running the restriction finder
over the soft masked sequence?

Can you post some example code to replicate the bug/annoyance?

If you think this is a genuine bug then please submit a biojava bug
report to http://bugzilla.open-bio.org/
Please also include the example code that demonstrates the bug.

Thanks.

- Mark

On 2/28/07, Ilhami Visne <ilhami.visne at gmail.com> wrote:
> i've changed my code and called the RestrictionSiteFinder with the new
> sequence. it's throwed this exception.
>
> Exception in thread "Thread-25"
> java.lang.UnsupportedOperationException: Ambiguity should be handled
> at the level of the wrapped Alphabet
>         at org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
>         at org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
>         at org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
>         at org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
>         at org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)
>
> i understand why it didn't work (lower case symbol 'a' and upper
> symbol 'A'), but i can't find a solution. Any idea?
>
> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> > Thank you. it does now. i should able to find it myself, but i am really
> > not a bioinformaticians yet.
> >
> > my code (maybe there is someone, who has the same problem like me)
> >
> > BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> >
> > Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
> > SymbolTokenization dnaParser = dna.getTokenization("token");
> >
> > RichSequenceIterator iter =
> > RichSequence.IOTools.readFasta(br,dnaParser,null);
> > RichSequence rs = iter.nextRichSequence();
> >
> > Mark Schreiber wrote:
> > > Hi -
> > >
> > > There are also the classes: SoftMaskedAlphabet and
> > > SoftMaskedAlphabet.CaseSensitiveTokenization and
> > > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
> > > read a sequence that contains case sensitive information and (if you
> > > wish) make use of that information. You can also write out the
> > > sequence in the original case sensitive format.
> > >
> > > It was originally designed for reading data that had been 'softmasked'
> > > for low complexity regions (eg lower case regions are low complexity
> > > and would be ignored in subsequent analysis) but it would be used for
> > > quality or any other distinction.
> > >
> > > - Mark
> > >
> > > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
> > >> Thank you for quick answer. Here is the part of my code:
> > >>
> > >> BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
> > >> RichSequenceIterator iter = RichSequence.IOTools.readFastaDNA(br,null);
> > >> RichSequence rs = iter.nextRichSequence();
> > >>
> > >> Richard Holland wrote:
> > >> > -----BEGIN PGP SIGNED MESSAGE-----
> > >> > Hash: SHA1
> > >> >
> > >> > DNA is not case-sensitive. What I suspect you are parsing is the
> > >> output
> > >> > of some sequencing software which is using case as a rough
> > >> indicator of
> > >> > base calling quality?
> > >> >
> > >> > The case will have been lost when the file was parsed, not at the
> > >> moment
> > >> > you iterate over the resulting sequences. This means that you have to
> > >> > modify your file parsing method to become case-sensitive.
> > >> >
> > >> > The default DNA alphabet is not case-sensitive. It makes no
> > >> distinction
> > >> > between the two, and will convert everything to one case.
> > >> >
> > >> > If you need to preserve case, you will need to use a custom alphabet
> > >> > which treats the cases differently, and also specify a tokenizer which
> > >> > is case-sensitive. See the help pages at http://biojava.org/ for
> > >> help on
> > >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
> > >> alphabet
> > >> > in BioJava, which interprets the case and stores the quality scores
> > >> > separately.
> > >> >
> > >> > Note however that your custom alphabet is NOT the same as the original
> > >> > DNA alphabet, and so you may not be able to use it in all the standard
> > >> > transforms (RNA etc.). If you do want to use these then you will
> > >> have to
> > >> > make a second copy of each sequence using the normal DNA alphabet and
> > >> > pass that copy to the routines.
> > >> >
> > >> > If you post to this list the code you are using to read the file,
> > >> then I
> > >> > can show you where to insert the reference to this new alphabet.
> > >> >
> > >> > cheers,
> > >> > Richard
> > >> >
> > >> > Ilhami Visne wrote:
> > >> >
> > >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
> > >> and i am
> > >> >> using now RichSequenceIterator to iterate over the sequences.
> > >> >>
> > >> >> How can i tell biojava that it should parse it case-sensitive? if
> > >> i call
> > >> >> seq.seqString() method, it should return exactly like it was in
> > >> the file
> > >> >> with upper- and lower-case.
> > >> >>
> > >> >> thanx.
> > >> >> _______________________________________________
> > >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >> >>
> > >> >>
> > >> > -----BEGIN PGP SIGNATURE-----
> > >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
> > >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
> > >> >
> > >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
> > >> > uZKlrdE8y6vMfKcOlm9yBZA=
> > >> > =2VZC
> > >> > -----END PGP SIGNATURE-----
> > >> >
> > >> >
> > >>
> > >> _______________________________________________
> > >> 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 alainfa at bluewin.ch  Wed Feb 28 13:54:17 2007
From: alainfa at bluewin.ch (Alain Favre)
Date: Wed, 28 Feb 2007 14:54:17 +0100
Subject: [Biojava-l] biojava.utils.bytecode
Message-ID: <000601c75b3f$f1409fc0$2101a8c0@camillealain>

Hello,
Looking for this package whwre can I find it
Thanks for your answer
A. Favre


From ilhami.visne at gmail.com  Wed Feb 28 19:56:36 2007
From: ilhami.visne at gmail.com (ilhami visne)
Date: Wed, 28 Feb 2007 20:56:36 +0100
Subject: [Biojava-l] case-sensitive sequences
In-Reply-To: <93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>
References: <ce6b4d120702270647s966cc6bh95d3b291359ea5ad@mail.gmail.com>	
	<45E44B6F.9090202@ebi.ac.uk> <45E47045.5010400@gmail.com>	
	<93b45ca50702271854h3253e04bw3e9ba2f98ddc1270@mail.gmail.com>	
	<45E51009.2090605@gmail.com>	
	<ce6b4d120702272348i54f6846cw29ee2e1e8b98b670@mail.gmail.com>
	<93b45ca50702280303j4480c8d4kd69c9aa41c0221d2@mail.gmail.com>
Message-ID: <45E5DE74.8040008@gmail.com>

Yes, there is one.

i am writing a small program, which my coworker will use. first it 
downloads some repeat masked sequences and then with 
restrictionsitefinder it finds cuts and then exports all fragments.  
these fragments should be repeat masked (case-sensitive) too. after i 
find the cut positions, with SequenceTools.subSequence() i'll extract 
the fragments and write them out.

here is the code sample:

BufferedReader br = new BufferedReader(new FileReader("aSeq.fasta"));
           
Alphabet maskeddna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
SymbolTokenization dnaParser = maskeddna.getTokenization("token");
           
RichSequenceIterator iter = 
RichSequence.IOTools.readFasta(br,dnaParser,null);
RichSequence seq = iter.nextRichSequence();
           
SimpleThreadPool threadPool = new SimpleThreadPool();
RestrictionEnzyme enzyme = RestrictionEnzymeManager.getEnzyme("MseI");
RestrictionMapper mapper = new RestrictionMapper(threadPool);

mapper.addEnzyme(enzyme);
mapper.annotate(seq);

this throws:

Exception in thread "Thread-3" java.lang.UnsupportedOperationException: 
Ambiguity should be handled at the level of the wrapped Alphabet
        at 
org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183)
        at 
org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223)
        at 
org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75)
        at 
org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73)
        at 
org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295)


Mark Schreiber wrote:
> Hi -
>
> Is there any reason why you need to be running the restriction finder
> over the soft masked sequence?
>
> Can you post some example code to replicate the bug/annoyance?
>
> If you think this is a genuine bug then please submit a biojava bug
> report to http://bugzilla.open-bio.org/
> Please also include the example code that demonstrates the bug.
>
> Thanks.
>
> - Mark
>
> On 2/28/07, Ilhami Visne <ilhami.visne at gmail.com> wrote:
>> i've changed my code and called the RestrictionSiteFinder with the new
>> sequence. it's throwed this exception.
>>
>> Exception in thread "Thread-25"
>> java.lang.UnsupportedOperationException: Ambiguity should be handled
>> at the level of the wrapped Alphabet
>>         at 
>> org.biojava.bio.symbol.SoftMaskedAlphabet.getAmbiguity(SoftMaskedAlphabet.java:183) 
>>
>>         at 
>> org.biojava.bio.symbol.AlphabetManager.getAllSymbols(AlphabetManager.java:223) 
>>
>>         at 
>> org.biojava.bio.seq.io.SymbolListCharSequence.<init>(SymbolListCharSequence.java:75) 
>>
>>         at 
>> org.biojava.bio.molbio.RestrictionSiteFinder.run(RestrictionSiteFinder.java:73) 
>>
>>         at 
>> org.biojava.utils.SimpleThreadPool$PooledThread.run(SimpleThreadPool.java:295) 
>>
>>
>> i understand why it didn't work (lower case symbol 'a' and upper
>> symbol 'A'), but i can't find a solution. Any idea?
>>
>> On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> > Thank you. it does now. i should able to find it myself, but i am 
>> really
>> > not a bioinformaticians yet.
>> >
>> > my code (maybe there is someone, who has the same problem like me)
>> >
>> > BufferedReader br = new BufferedReader(new FileReader("seq.fasta"));
>> >
>> > Alphabet dna = SoftMaskedAlphabet.getInstance(DNATools.getDNA());
>> > SymbolTokenization dnaParser = dna.getTokenization("token");
>> >
>> > RichSequenceIterator iter =
>> > RichSequence.IOTools.readFasta(br,dnaParser,null);
>> > RichSequence rs = iter.nextRichSequence();
>> >
>> > Mark Schreiber wrote:
>> > > Hi -
>> > >
>> > > There are also the classes: SoftMaskedAlphabet and
>> > > SoftMaskedAlphabet.CaseSensitiveTokenization and
>> > > SoftMaskedAlphabet.MaskingDetector. Together these classes let you
>> > > read a sequence that contains case sensitive information and (if you
>> > > wish) make use of that information. You can also write out the
>> > > sequence in the original case sensitive format.
>> > >
>> > > It was originally designed for reading data that had been 
>> 'softmasked'
>> > > for low complexity regions (eg lower case regions are low complexity
>> > > and would be ignored in subsequent analysis) but it would be used 
>> for
>> > > quality or any other distinction.
>> > >
>> > > - Mark
>> > >
>> > > On 2/28/07, ilhami visne <ilhami.visne at gmail.com> wrote:
>> > >> Thank you for quick answer. Here is the part of my code:
>> > >>
>> > >> BufferedReader br = new BufferedReader(new 
>> FileReader("seq.fasta"));
>> > >> RichSequenceIterator iter = 
>> RichSequence.IOTools.readFastaDNA(br,null);
>> > >> RichSequence rs = iter.nextRichSequence();
>> > >>
>> > >> Richard Holland wrote:
>> > >> > -----BEGIN PGP SIGNED MESSAGE-----
>> > >> > Hash: SHA1
>> > >> >
>> > >> > DNA is not case-sensitive. What I suspect you are parsing is the
>> > >> output
>> > >> > of some sequencing software which is using case as a rough
>> > >> indicator of
>> > >> > base calling quality?
>> > >> >
>> > >> > The case will have been lost when the file was parsed, not at the
>> > >> moment
>> > >> > you iterate over the resulting sequences. This means that you 
>> have to
>> > >> > modify your file parsing method to become case-sensitive.
>> > >> >
>> > >> > The default DNA alphabet is not case-sensitive. It makes no
>> > >> distinction
>> > >> > between the two, and will convert everything to one case.
>> > >> >
>> > >> > If you need to preserve case, you will need to use a custom 
>> alphabet
>> > >> > which treats the cases differently, and also specify a 
>> tokenizer which
>> > >> > is case-sensitive. See the help pages at http://biojava.org/ for
>> > >> help on
>> > >> > creating new alphabets. Or, have a look at the ABITools.QUALITY
>> > >> alphabet
>> > >> > in BioJava, which interprets the case and stores the quality 
>> scores
>> > >> > separately.
>> > >> >
>> > >> > Note however that your custom alphabet is NOT the same as the 
>> original
>> > >> > DNA alphabet, and so you may not be able to use it in all the 
>> standard
>> > >> > transforms (RNA etc.). If you do want to use these then you will
>> > >> have to
>> > >> > make a second copy of each sequence using the normal DNA 
>> alphabet and
>> > >> > pass that copy to the routines.
>> > >> >
>> > >> > If you post to this list the code you are using to read the file,
>> > >> then I
>> > >> > can show you where to insert the reference to this new alphabet.
>> > >> >
>> > >> > cheers,
>> > >> > Richard
>> > >> >
>> > >> > Ilhami Visne wrote:
>> > >> >
>> > >> >> my sequence files contain case-sensitive symbols (TAATAACgagagg)
>> > >> and i am
>> > >> >> using now RichSequenceIterator to iterate over the sequences.
>> > >> >>
>> > >> >> How can i tell biojava that it should parse it 
>> case-sensitive? if
>> > >> i call
>> > >> >> seq.seqString() method, it should return exactly like it was in
>> > >> the file
>> > >> >> with upper- and lower-case.
>> > >> >>
>> > >> >> thanx.
>> > >> >> _______________________________________________
>> > >> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > >> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> > >> >>
>> > >> >>
>> > >> > -----BEGIN PGP SIGNATURE-----
>> > >> > Version: GnuPG v1.4.2.2 (GNU/Linux)
>> > >> > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>> > >> >
>> > >> > iD8DBQFF5Etv4C5LeMEKA/QRAnGBAJ45eeQhmb4AT0CLTQCVyn5HxFS/cQCfXXgv
>> > >> > uZKlrdE8y6vMfKcOlm9yBZA=
>> > >> > =2VZC
>> > >> > -----END PGP SIGNATURE-----
>> > >> >
>> > >> >
>> > >>
>> > >> _______________________________________________
>> > >> 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
>>
>