From jjramirez at estudiantes.uci.cu  Mon May  6 21:41:45 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 06 May 2013 21:41:45 -0400 (EDT)
Subject: [Biojava-l] AMOScmp problem
Message-ID: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>

Hi !
I'm interested in the reference based assemblies using AMOScmp, I used tarchive2Amos to obtain the .afg file an I have the reference (.fasta file), but the problem is that the output files (.fasta and .contig) are empty. In the log files there is a WARNING which says that the file FRG.ifo was not found and could not retrieve mate pairs information.
This is very important to me and won't have many time for that.

Please any sugestion for this proble ?

Thanks in advance

-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu


From sbliven at ucsd.edu  Tue May  7 15:00:44 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 7 May 2013 12:00:44 -0700
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>
References: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>
Message-ID: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>

Hey Janier,

Sorry no one responded to your last question. Biojava doesn't currently do
full-blown assembly, although the basic pairwise alignment algorithms are
there.

I've never used AMOScmp myself, and so can't advise you on your problem.

-Spencer


On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> Hi !
> I'm interested in the reference based assemblies using AMOScmp, I used
> tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> file), but the problem is that the output files (.fasta and .contig) are
> empty. In the log files there is a WARNING which says that the file FRG.ifo
> was not found and could not retrieve mate pairs information.
> This is very important to me and won't have many time for that.
>
> Please any sugestion for this proble ?
>
> Thanks in advance
>
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From sbliven at ucsd.edu  Tue May  7 16:27:22 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 7 May 2013 13:27:22 -0700
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
References: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>
	<54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
Message-ID: <CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>

Janier,

Biojava 1 is only receiving bug fixes currently. There are a couple changes
since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
maven repository. There is no release date for 3.0.6 yet, but again you can
use the latest SNAPSHOT from maven if you need new features.


-Spencer


On Tue, May 7, 2013 at 12:31 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> When Biojaba 1.8.3 will be released ?
>
> cheers
>
>
> ----- Mensaje original -----
> De: "Spencer Bliven" <sbliven at ucsd.edu>
> Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
> CC: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> Enviados: Martes, 7 de Mayo 2013 21:00:44
> Asunto: Re: [Biojava-l] AMOScmp problem
>
>
>
>
> Hey Janier,
>
> Sorry no one responded to your last question. Biojava doesn't currently do
> full-blown assembly, although the basic pairwise alignment algorithms are
> there.
>
> I've never used AMOScmp myself, and so can't advise you on your problem.
>
> -Spencer
>
>
>
>
> On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
> jjramirez at estudiantes.uci.cu > wrote:
>
>
> Hi !
> I'm interested in the reference based assemblies using AMOScmp, I used
> tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> file), but the problem is that the output files (.fasta and .contig) are
> empty. In the log files there is a WARNING which says that the file FRG.ifo
> was not found and could not retrieve mate pairs information.
> This is very important to me and won't have many time for that.
>
> Please any sugestion for this proble ?
>
> Thanks in advance
>
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> http://www.uci.cu
>


From heuermh at gmail.com  Tue May  7 16:43:10 2013
From: heuermh at gmail.com (Michael Heuer)
Date: Tue, 7 May 2013 15:43:10 -0500
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>
References: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>
	<54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
	<CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>
Message-ID: <CAOjYwMwnX+E0rf7bPtmBLowZY0dqdpvEWa4=5NufZ5wjgNn4AA@mail.gmail.com>

Hello Spencer, Janier

I suppose there will be a biojava-legacy 1.8.3 release as soon as we figure
out the configuration changes necessary to support the release process due
to the svn --> github switch.

   michael


On Tue, May 7, 2013 at 3:27 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Janier,
>
> Biojava 1 is only receiving bug fixes currently. There are a couple changes
> since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
> maven repository. There is no release date for 3.0.6 yet, but again you can
> use the latest SNAPSHOT from maven if you need new features.
>
>
> -Spencer
>
>
> On Tue, May 7, 2013 at 12:31 PM, Janier J. Ram?rez <
> jjramirez at estudiantes.uci.cu> wrote:
>
> > When Biojaba 1.8.3 will be released ?
> >
> > cheers
> >
> >
> > ----- Mensaje original -----
> > De: "Spencer Bliven" <sbliven at ucsd.edu>
> > Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
> > CC: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> > Enviados: Martes, 7 de Mayo 2013 21:00:44
> > Asunto: Re: [Biojava-l] AMOScmp problem
> >
> >
> >
> >
> > Hey Janier,
> >
> > Sorry no one responded to your last question. Biojava doesn't currently
> do
> > full-blown assembly, although the basic pairwise alignment algorithms are
> > there.
> >
> > I've never used AMOScmp myself, and so can't advise you on your problem.
> >
> > -Spencer
> >
> >
> >
> >
> > On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
> > jjramirez at estudiantes.uci.cu > wrote:
> >
> >
> > Hi !
> > I'm interested in the reference based assemblies using AMOScmp, I used
> > tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> > file), but the problem is that the output files (.fasta and .contig) are
> > empty. In the log files there is a WARNING which says that the file
> FRG.ifo
> > was not found and could not retrieve mate pairs information.
> > This is very important to me and won't have many time for that.
> >
> > Please any sugestion for this proble ?
> >
> > Thanks in advance
> >
> > --
> >
> >
> > Universidad de las Ciencias Inform?ticas
> > Janier J. Ram?rez Landaburo
> > Facultad - 6
> > Tel-837-3121
> > http://www.uci.cu
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > http://www.uci.cu
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From jjramirez at estudiantes.uci.cu  Tue May  7 23:51:33 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Tue, 07 May 2013 23:51:33 -0400 (EDT)
Subject: [Biojava-l] Getting reverse complement
In-Reply-To: <bc78d382-0b1b-40fe-868b-1f2772730fd7@ucimail4.uci.cu>
Message-ID: <cfacbb92-53d2-4b55-b410-08b95c6139fd@ucimail4.uci.cu>

I'm triyng to get the reverse complement from a sequence with gaps (represented as ':'), but biojava thow an IllegalSymbolException, is this a bug or what is the symbol to represent gaps in biojava ?

Here is the error.


org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: ':'
	at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
	at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
	at org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
	at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)


Greetings

Janier

-- 

Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu


From biojava at hannes.oib.com  Wed May  8 00:21:33 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 8 May 2013 06:21:33 +0200
Subject: [Biojava-l] Getting reverse complement
In-Reply-To: <f326f8c7-a787-4dec-ac38-ea09c58a0f3a@ucimail4.uci.cu>
References: <CAPXi2mnoSvBk8FZ8hWFi_KTwoHuob9MBAMzU5_e9rX5qsgk2yw@mail.gmail.com>
	<f326f8c7-a787-4dec-ac38-ea09c58a0f3a@ucimail4.uci.cu>
Message-ID: <CAPXi2mk6tTMpJjr9SFmSY8vTANVmVcJia+8mmqWX5b+jGbwntA@mail.gmail.com>

I missed posting my answer to the list too.


Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ram?rez :

> Yes, already it works fine, thanks !
>
> Janier
>
> ----- Mensaje original -----
> De: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com <javascript:;>>
> Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu <javascript:;>>
> Enviados: Mi?rcoles, 8 de Mayo 2013 5:59:54
> Asunto: [Biojava-l] Getting reverse complement
>
> Usually, gaps are signified by - (probably . works too)
>
>
>
>
> Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ram?rez :
>
>
> I'm triyng to get the reverse complement from a sequence with gaps
> (represented as ':'), but biojava thow an IllegalSymbolException, is this a
> bug or what is the symbol to represent gaps in biojava ?
>
> Here is the error.
>
>
> org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
> contain character: ':'
> at
> org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
> at
> org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
> at
> org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
> at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)
>
>
> Greetings
>
> Janier
>
> --
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org <javascript:;>
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> http://www.uci.cu
>


From jjramirez at estudiantes.uci.cu  Mon May 13 10:21:38 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 13 May 2013 10:21:38 -0400 (EDT)
Subject: [Biojava-l] File formats parser
In-Reply-To: <5197d2e9-31f1-4518-811f-7b7992d9e53f@ucimail4.uci.cu>
Message-ID: <935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>

There is in Biojava a parser for some of the next file formats ?? :
.sam
.bam
.gig
.ace 


thanks in advance
-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu


From p.j.a.cock at googlemail.com  Mon May 13 12:17:56 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 May 2013 17:17:56 +0100
Subject: [Biojava-l] File formats parser
In-Reply-To: <935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>
References: <5197d2e9-31f1-4518-811f-7b7992d9e53f@ucimail4.uci.cu>
	<935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>
Message-ID: <CAKVJ-_4ArgA_weC1F8YJr+6NM+b9_F9FExb_FWgb=oZ4ErdWng@mail.gmail.com>

On Mon, May 13, 2013 at 3:21 PM, Janier J. Ram?rez
<jjramirez at estudiantes.uci.cu> wrote:
> There is in Biojava a parser for some of the next file formats ?? :
> .sam
> .bam
> ...

I'm not sure what exactly is in BioJava for these formats, but I would
suggest you (also) consider Picard for working with SAM/BAM in Java.

Peter


From hlapp at drycafe.net  Wed May 15 16:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Biojava-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================




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From andreas at sdsc.edu  Thu May 16 00:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Biojava-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>

From p.j.a.cock at googlemail.com  Thu May 16 05:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Biojava-l] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter

From jjramirez at estudiantes.uci.cu  Thu May 16 09:51:52 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Thu, 16 May 2013 09:51:52 -0400 (EDT)
Subject: [Biojava-l] help with fastq
In-Reply-To: <23602a14-84c7-4b34-ad02-9a6d64f8d50d@ucimail4.uci.cu>
Message-ID: <0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>

Hi again comunity !

I need this time generate a Fastq file from many fasta files, using illumina scores (one default value).
I ?ve tried this but am having a problem wthis the header and the identifier of the file.
makes Biojava this work ?

greetings

Janier
-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu


From biojava at hannes.oib.com  Thu May 16 14:45:48 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 16 May 2013 20:45:48 +0200
Subject: [Biojava-l] help with fastq
In-Reply-To: <0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>
References: <23602a14-84c7-4b34-ad02-9a6d64f8d50d@ucimail4.uci.cu>
	<0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>
Message-ID: <CAPXi2mmtv7Tpdj4FHCKnzCiRFho6x+zzERM3EKxOtdixX5f-8Q@mail.gmail.com>

Can you show some code, so we can see where the problem is?


On Thu, May 16, 2013 at 3:51 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> Hi again comunity !
>
> I need this time generate a Fastq file from many fasta files, using
> illumina scores (one default value).
> I ?ve tried this but am having a problem wthis the header and the
> identifier of the file.
> makes Biojava this work ?
>
> greetings
>
> Janier
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From bbimber at gmail.com  Thu May 23 14:53:48 2013
From: bbimber at gmail.com (Ben Bimber)
Date: Thu, 23 May 2013 11:53:48 -0700
Subject: [Biojava-l] reading genbank data
Message-ID: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>

Hello,

To date, I have used BioJava3 for very limited work such as read/writing
FASTA files.  I am trying to determine the best method to read and parse
sequence in genbank format using java.  As far as i can tell, legacy
BioJava has classes to support this (RichSequence.IOTools); however, I do
not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
have support for parsing genbank files?

Thanks in advance for any help.

-Ben

From biojava at hannes.oib.com  Thu May 23 16:14:39 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 23 May 2013 22:14:39 +0200
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
Message-ID: <CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>

Well, it doesn't look like that was ported to biojava 3 yet.

We'll add that to the todo list?


On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:

> Hello,
>
> To date, I have used BioJava3 for very limited work such as read/writing
> FASTA files.  I am trying to determine the best method to read and parse
> sequence in genbank format using java.  As far as i can tell, legacy
> BioJava has classes to support this (RichSequence.IOTools); however, I do
> not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
> have support for parsing genbank files?
>
> Thanks in advance for any help.
>
> -Ben
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From andreas at sdsc.edu  Fri May 24 01:36:10 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 23 May 2013 22:36:10 -0700
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
	<CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
Message-ID: <CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>

Hi Hannes,

would you be interested in taking this one on?

Thanks,

Andreas


On Thu, May 23, 2013 at 1:14 PM, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Well, it doesn't look like that was ported to biojava 3 yet.
>
> We'll add that to the todo list?
>
>
> On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:
>
> > Hello,
> >
> > To date, I have used BioJava3 for very limited work such as read/writing
> > FASTA files.  I am trying to determine the best method to read and parse
> > sequence in genbank format using java.  As far as i can tell, legacy
> > BioJava has classes to support this (RichSequence.IOTools); however, I do
> > not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
> > have support for parsing genbank files?
> >
> > Thanks in advance for any help.
> >
> > -Ben
> > _______________________________________________
> > 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 biojava at hannes.oib.com  Fri May 24 03:09:05 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 24 May 2013 09:09:05 +0200
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
	<CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
	<CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>
Message-ID: <CAPXi2mnt-u1V6uF_rT=kmYBA9ZG1GhJCFde1mrXjT+beT0_qkQ@mail.gmail.com>

I still need to finish up the last task (unfortunately I'm a bit short on
spare time currently) but I guess since it's parsing, I could work on
that...

Hannes


On Fri, May 24, 2013 at 7:36 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Hannes,
>
> would you be interested in taking this one on?
>
> Thanks,
>
> Andreas
>
>
> On Thu, May 23, 2013 at 1:14 PM, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
>
>> Well, it doesn't look like that was ported to biojava 3 yet.
>>
>> We'll add that to the todo list?
>>
>>
>> On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:
>>
>> > Hello,
>> >
>> > To date, I have used BioJava3 for very limited work such as read/writing
>> > FASTA files.  I am trying to determine the best method to read and parse
>> > sequence in genbank format using java.  As far as i can tell, legacy
>> > BioJava has classes to support this (RichSequence.IOTools); however, I
>> do
>> > not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
>> > have support for parsing genbank files?
>> >
>> > Thanks in advance for any help.
>> >
>> > -Ben
>> > _______________________________________________
>> > 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 sagayanilo at gmail.com  Wed May 29 07:52:51 2013
From: sagayanilo at gmail.com (Christina Nilofer)
Date: Wed, 29 May 2013 17:22:51 +0530
Subject: [Biojava-l] Regarding the transcription script
Message-ID: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>

Hi Sir,

This is christina,

In your code for transcription input was "atgccgaatcgtaa"
and the output was   "augccgaaucguaa".
 Here in this you have replaced t's with u's but the output must be
"uacggcuuagcauu"


we are not changing dna to rna, we are transcribing.

-- 
*Christy*
**
**

From amr_alhossary at hotmail.com  Wed May 29 08:00:06 2013
From: amr_alhossary at hotmail.com (Amr AL-HOSSARY)
Date: Wed, 29 May 2013 20:00:06 +0800
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
Message-ID: <BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>

Here is the definition of transcription from Wikipedia:

"Transcription is the first step of gene expression, in which a particular
segment of DNA is copied into RNA by the enzyme, RNA polymerase"


http://en.wikipedia.org/wiki/Transcription_(genetics)

Regards

Amr

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Christina Nilofer
Sent: Wednesday, May 29, 2013 7:53 PM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Regarding the transcription script

Hi Sir,

This is christina,

In your code for transcription input was "atgccgaatcgtaa"
and the output was   "augccgaaucguaa".
 Here in this you have replaced t's with u's but the output must be
"uacggcuuagcauu"


we are not changing dna to rna, we are transcribing.

--
*Christy*
**
**
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l

From dasarnow at gmail.com  Wed May 29 13:42:44 2013
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Wed, 29 May 2013 10:42:44 -0700
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
	<BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
Message-ID: <CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>

And the third sentence from that article is:  "during transcription, a DNA
sequence is read by an RNA polymerase, which produces a *complementary*,
antiparallel RNA strand."

mRNA is complementary to the *non-coding* strand. If the original sequence
is coding, you just change T and U. If not, you must make a complement
containing U.

The example sequence is clearly coding, thus the confusion.

-da


On Wed, May 29, 2013 at 5:00 AM, Amr AL-HOSSARY
<amr_alhossary at hotmail.com>wrote:

> Here is the definition of transcription from Wikipedia:
>
> "Transcription is the first step of gene expression, in which a particular
> segment of DNA is copied into RNA by the enzyme, RNA polymerase"
>
>
> http://en.wikipedia.org/wiki/Transcription_(genetics)
>
> Regards
>
> Amr
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Christina
> Nilofer
> Sent: Wednesday, May 29, 2013 7:53 PM
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Regarding the transcription script
>
> Hi Sir,
>
> This is christina,
>
> In your code for transcription input was "atgccgaatcgtaa"
> and the output was   "augccgaaucguaa".
>  Here in this you have replaced t's with u's but the output must be
> "uacggcuuagcauu"
>
>
> we are not changing dna to rna, we are transcribing.
>
> --
> *Christy*
> **
> **
> _______________________________________________
> 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 p.j.a.cock at googlemail.com  Wed May 29 14:44:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 May 2013 19:44:10 +0100
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
	<BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
	<CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>
Message-ID: <CAKVJ-_53hbNQibd5DhbC69p1Y2Rk8HjmQCUycRaN40yBSsw1_Q@mail.gmail.com>

On Wed, May 29, 2013 at 6:42 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> And the third sentence from that article is:  "during transcription, a DNA
> sequence is read by an RNA polymerase, which produces a *complementary*,
> antiparallel RNA strand."
>
> mRNA is complementary to the *non-coding* strand. If the original sequence
> is coding, you just change T and U. If not, you must make a complement
> containing U.
>
> The example sequence is clearly coding, thus the confusion.
>
> -da

Hi Christina and all,

This has come up on the Biopython mailing list a few times too.
Does the strand section in the Biopython tutorial help at all?

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc24

"Before talking about transcription, I want to try and clarify the
strand issue. Consider the following (made up) stretch of double
stranded DNA which encodes a short peptide: ...
The actual biological transcription process works from the
template strand, doing a reverse complement (TCAG -> CUGA)
to give the mRNA. However, in Biopython and bioinformatics
in general, we typically work directly with the coding strand
because this means we can get the mRNA sequence just
by switching T -> U."

Regards,

Peter

From sagayanilo at gmail.com  Wed May 29 23:39:08 2013
From: sagayanilo at gmail.com (Christina Nilofer)
Date: Thu, 30 May 2013 09:09:08 +0530
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
Message-ID: <CAOU5aeoCP_=rvrWo3ir36R+LreB7KDWAeoT7+6rCCdnfssgbNg@mail.gmail.com>

Thank you for the reply sir, now I am able to understand the concept
better, thank you sirs.

On Wed, May 29, 2013 at 5:22 PM, Christina Nilofer <sagayanilo at gmail.com>wrote:

> Hi Sir,
>
> This is christina,
>
> In your code for transcription input was "atgccgaatcgtaa"
> and the output was   "augccgaaucguaa".
>  Here in this you have replaced t's with u's but the output must be
> "uacggcuuagcauu"
>
>
> we are not changing dna to rna, we are transcribing.
>
> --
> *Christy*
> **
> **
>
>



-- 
*Christy*
**
**

From jjramirez at estudiantes.uci.cu  Tue May  7 01:41:45 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 06 May 2013 21:41:45 -0400 (EDT)
Subject: [Biojava-l] AMOScmp problem
Message-ID: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>

Hi !
I'm interested in the reference based assemblies using AMOScmp, I used tarchive2Amos to obtain the .afg file an I have the reference (.fasta file), but the problem is that the output files (.fasta and .contig) are empty. In the log files there is a WARNING which says that the file FRG.ifo was not found and could not retrieve mate pairs information.
This is very important to me and won't have many time for that.

Please any sugestion for this proble ?

Thanks in advance

-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu



From sbliven at ucsd.edu  Tue May  7 19:00:44 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 7 May 2013 12:00:44 -0700
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>
References: <d11a77b1-9fd6-4c46-a7df-fcdd141bd4fb@ucimail4.uci.cu>
Message-ID: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>

Hey Janier,

Sorry no one responded to your last question. Biojava doesn't currently do
full-blown assembly, although the basic pairwise alignment algorithms are
there.

I've never used AMOScmp myself, and so can't advise you on your problem.

-Spencer


On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> Hi !
> I'm interested in the reference based assemblies using AMOScmp, I used
> tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> file), but the problem is that the output files (.fasta and .contig) are
> empty. In the log files there is a WARNING which says that the file FRG.ifo
> was not found and could not retrieve mate pairs information.
> This is very important to me and won't have many time for that.
>
> Please any sugestion for this proble ?
>
> Thanks in advance
>
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From sbliven at ucsd.edu  Tue May  7 20:27:22 2013
From: sbliven at ucsd.edu (Spencer Bliven)
Date: Tue, 7 May 2013 13:27:22 -0700
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
References: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>
	<54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
Message-ID: <CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>

Janier,

Biojava 1 is only receiving bug fixes currently. There are a couple changes
since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
maven repository. There is no release date for 3.0.6 yet, but again you can
use the latest SNAPSHOT from maven if you need new features.


-Spencer


On Tue, May 7, 2013 at 12:31 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> When Biojaba 1.8.3 will be released ?
>
> cheers
>
>
> ----- Mensaje original -----
> De: "Spencer Bliven" <sbliven at ucsd.edu>
> Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
> CC: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> Enviados: Martes, 7 de Mayo 2013 21:00:44
> Asunto: Re: [Biojava-l] AMOScmp problem
>
>
>
>
> Hey Janier,
>
> Sorry no one responded to your last question. Biojava doesn't currently do
> full-blown assembly, although the basic pairwise alignment algorithms are
> there.
>
> I've never used AMOScmp myself, and so can't advise you on your problem.
>
> -Spencer
>
>
>
>
> On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
> jjramirez at estudiantes.uci.cu > wrote:
>
>
> Hi !
> I'm interested in the reference based assemblies using AMOScmp, I used
> tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> file), but the problem is that the output files (.fasta and .contig) are
> empty. In the log files there is a WARNING which says that the file FRG.ifo
> was not found and could not retrieve mate pairs information.
> This is very important to me and won't have many time for that.
>
> Please any sugestion for this proble ?
>
> Thanks in advance
>
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> http://www.uci.cu
>



From heuermh at gmail.com  Tue May  7 20:43:10 2013
From: heuermh at gmail.com (Michael Heuer)
Date: Tue, 7 May 2013 15:43:10 -0500
Subject: [Biojava-l] AMOScmp problem
In-Reply-To: <CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>
References: <CA+P6ar=HH+aU8z7HbFf-GHu7ENQpOxxVSevwp-FrogYB05C_fg@mail.gmail.com>
	<54b07773-dbda-46de-8bdf-b15819c92a7e@ucimail4.uci.cu>
	<CA+P6arn0QGN4Y3Wgz-zZP6UkFUXgHoPvJBDj-KenOjSvoFkDoA@mail.gmail.com>
Message-ID: <CAOjYwMwnX+E0rf7bPtmBLowZY0dqdpvEWa4=5NufZ5wjgNn4AA@mail.gmail.com>

Hello Spencer, Janier

I suppose there will be a biojava-legacy 1.8.3 release as soon as we figure
out the configuration changes necessary to support the release process due
to the svn --> github switch.

   michael


On Tue, May 7, 2013 at 3:27 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Janier,
>
> Biojava 1 is only receiving bug fixes currently. There are a couple changes
> since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
> maven repository. There is no release date for 3.0.6 yet, but again you can
> use the latest SNAPSHOT from maven if you need new features.
>
>
> -Spencer
>
>
> On Tue, May 7, 2013 at 12:31 PM, Janier J. Ram?rez <
> jjramirez at estudiantes.uci.cu> wrote:
>
> > When Biojaba 1.8.3 will be released ?
> >
> > cheers
> >
> >
> > ----- Mensaje original -----
> > De: "Spencer Bliven" <sbliven at ucsd.edu>
> > Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu>
> > CC: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> > Enviados: Martes, 7 de Mayo 2013 21:00:44
> > Asunto: Re: [Biojava-l] AMOScmp problem
> >
> >
> >
> >
> > Hey Janier,
> >
> > Sorry no one responded to your last question. Biojava doesn't currently
> do
> > full-blown assembly, although the basic pairwise alignment algorithms are
> > there.
> >
> > I've never used AMOScmp myself, and so can't advise you on your problem.
> >
> > -Spencer
> >
> >
> >
> >
> > On Mon, May 6, 2013 at 6:41 PM, Janier J. Ram?rez <
> > jjramirez at estudiantes.uci.cu > wrote:
> >
> >
> > Hi !
> > I'm interested in the reference based assemblies using AMOScmp, I used
> > tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> > file), but the problem is that the output files (.fasta and .contig) are
> > empty. In the log files there is a WARNING which says that the file
> FRG.ifo
> > was not found and could not retrieve mate pairs information.
> > This is very important to me and won't have many time for that.
> >
> > Please any sugestion for this proble ?
> >
> > Thanks in advance
> >
> > --
> >
> >
> > Universidad de las Ciencias Inform?ticas
> > Janier J. Ram?rez Landaburo
> > Facultad - 6
> > Tel-837-3121
> > http://www.uci.cu
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > http://www.uci.cu
> >
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From jjramirez at estudiantes.uci.cu  Wed May  8 03:51:33 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Tue, 07 May 2013 23:51:33 -0400 (EDT)
Subject: [Biojava-l] Getting reverse complement
In-Reply-To: <bc78d382-0b1b-40fe-868b-1f2772730fd7@ucimail4.uci.cu>
Message-ID: <cfacbb92-53d2-4b55-b410-08b95c6139fd@ucimail4.uci.cu>

I'm triyng to get the reverse complement from a sequence with gaps (represented as ':'), but biojava thow an IllegalSymbolException, is this a bug or what is the symbol to represent gaps in biojava ?

Here is the error.


org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: ':'
	at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
	at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
	at org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
	at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)


Greetings

Janier

-- 

Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu



From biojava at hannes.oib.com  Wed May  8 04:21:33 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 8 May 2013 06:21:33 +0200
Subject: [Biojava-l] Getting reverse complement
In-Reply-To: <f326f8c7-a787-4dec-ac38-ea09c58a0f3a@ucimail4.uci.cu>
References: <CAPXi2mnoSvBk8FZ8hWFi_KTwoHuob9MBAMzU5_e9rX5qsgk2yw@mail.gmail.com>
	<f326f8c7-a787-4dec-ac38-ea09c58a0f3a@ucimail4.uci.cu>
Message-ID: <CAPXi2mk6tTMpJjr9SFmSY8vTANVmVcJia+8mmqWX5b+jGbwntA@mail.gmail.com>

I missed posting my answer to the list too.


Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ram?rez :

> Yes, already it works fine, thanks !
>
> Janier
>
> ----- Mensaje original -----
> De: "Hannes Brandst?tter-M?ller" <biojava at hannes.oib.com <javascript:;>>
> Para: "Janier J. Ram?rez" <jjramirez at estudiantes.uci.cu <javascript:;>>
> Enviados: Mi?rcoles, 8 de Mayo 2013 5:59:54
> Asunto: [Biojava-l] Getting reverse complement
>
> Usually, gaps are signified by - (probably . works too)
>
>
>
>
> Am Mittwoch, 8. Mai 2013 schrieb Janier J. Ram?rez :
>
>
> I'm triyng to get the reverse complement from a sequence with gaps
> (represented as ':'), but biojava thow an IllegalSymbolException, is this a
> bug or what is the symbol to represent gaps in biojava ?
>
> Here is the error.
>
>
> org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't
> contain character: ':'
> at
> org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:175)
> at
> org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:246)
> at
> org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:178)
> at org.biojava.bio.seq.DNATools.createDNA(DNATools.java:204)
>
>
> Greetings
>
> Janier
>
> --
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org <javascript:;>
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> http://www.uci.cu
>



From jjramirez at estudiantes.uci.cu  Mon May 13 14:21:38 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Mon, 13 May 2013 10:21:38 -0400 (EDT)
Subject: [Biojava-l] File formats parser
In-Reply-To: <5197d2e9-31f1-4518-811f-7b7992d9e53f@ucimail4.uci.cu>
Message-ID: <935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>

There is in Biojava a parser for some of the next file formats ?? :
.sam
.bam
.gig
.ace 


thanks in advance
-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu



From p.j.a.cock at googlemail.com  Mon May 13 16:17:56 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 13 May 2013 17:17:56 +0100
Subject: [Biojava-l] File formats parser
In-Reply-To: <935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>
References: <5197d2e9-31f1-4518-811f-7b7992d9e53f@ucimail4.uci.cu>
	<935a748e-f958-4efa-8e51-658c333ce796@ucimail4.uci.cu>
Message-ID: <CAKVJ-_4ArgA_weC1F8YJr+6NM+b9_F9FExb_FWgb=oZ4ErdWng@mail.gmail.com>

On Mon, May 13, 2013 at 3:21 PM, Janier J. Ram?rez
<jjramirez at estudiantes.uci.cu> wrote:
> There is in Biojava a parser for some of the next file formats ?? :
> .sam
> .bam
> ...

I'm not sure what exactly is in BioJava for these formats, but I would
suggest you (also) consider Picard for working with SAM/BAM in Java.

Peter



From hlapp at drycafe.net  Wed May 15 20:44:07 2013
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Wed, 15 May 2013 16:44:07 -0400
Subject: [Biojava-l] Workshop on Sustainable Software for Science: Practice
	and Experiences
Message-ID: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>

FYI, if you haven't seen this yet:

http://wssspe.researchcomputing.org.uk/

It seems to me that the Bio* projects, perhaps led by BioPerl as the oldest and thus longest running (nowadays more fancily called "sustained") of them would have a lot to say about the subject. Anyone interested in a joint submission?

Also, I notice that Biojava's Andreas is on the organizing committee, so maybe he's been conspiring on something already :-)

	-hilmar
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================




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From andreas at sdsc.edu  Thu May 16 04:31:34 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 15 May 2013 21:31:34 -0700
Subject: [Biojava-l] Workshop on Sustainable Software for Science:
 Practice and Experiences
In-Reply-To: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
Message-ID: <CALthepxHNLm4eHJcCQ4dLnhJr5OhGJJEKTAjH+x7Ppq0oFFnDA@mail.gmail.com>

Thanks Hilmar, you were faster than me in sending this out..

You are right, it would be very interesting to hear what some of the long
running open-bio projects have to say on the topic of sustainability. Let
me know if anybody is interested in a submission!

Andreas




On Wed, May 15, 2013 at 1:44 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:

> FYI, if you haven't seen this yet:
>
> http://wssspe.researchcomputing.org.uk/
>
> It seems to me that the Bio* projects, perhaps led by BioPerl as the
> oldest and thus longest running (nowadays more fancily called "sustained")
> of them would have a lot to say about the subject. Anyone interested in a
> joint submission?
>
> Also, I notice that Biojava's Andreas is on the organizing committee, so
> maybe he's been conspiring on something already :-)
>
>         -hilmar
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>


From p.j.a.cock at googlemail.com  Thu May 16 09:10:25 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 16 May 2013 10:10:25 +0100
Subject: [Biojava-l] [Bioperl-l] Workshop on Sustainable Software for
 Science: Practice and Experiences
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
References: <F3E4D752-EFC8-4C4E-98C8-F2FFA955F546@drycafe.net>
	<118F034CF4C3EF48A96F86CE585B94BF74E1F8C8@CHIMBX5.ad.uillinois.edu>
Message-ID: <CAKVJ-_4=xseYz+2pZzVaEC7uiWnN7H0umUAJvZX8Ouaoa3FbRw@mail.gmail.com>

On Thu, May 16, 2013 at 5:43 AM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Jason and I have discussed looking into opportunity's like this, I think it makes
> sense to try a joint submission.
>
> chris

This sounds like a good idea, although given the time and place I am
unlikely to be able to attend in person:

First Workshop on Sustainable Software for Science: Practice and
Experiences (WSSSPE)
(to held in conjunction with SC13, Sunday, 17 November 2013, Denver, CO, USA)
http://wssspe.researchcomputing.org.uk/

Rather than trying to discuss this over four mailing lists should we switch
to the cross project list open-bio-l, or continue off-list?
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Thanks,

Peter


From jjramirez at estudiantes.uci.cu  Thu May 16 13:51:52 2013
From: jjramirez at estudiantes.uci.cu (Janier =?utf-8?Q?J=2E_Ram=C3=ADrez?=)
Date: Thu, 16 May 2013 09:51:52 -0400 (EDT)
Subject: [Biojava-l] help with fastq
In-Reply-To: <23602a14-84c7-4b34-ad02-9a6d64f8d50d@ucimail4.uci.cu>
Message-ID: <0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>

Hi again comunity !

I need this time generate a Fastq file from many fasta files, using illumina scores (one default value).
I ?ve tried this but am having a problem wthis the header and the identifier of the file.
makes Biojava this work ?

greetings

Janier
-- 


Universidad de las Ciencias Inform?ticas 
Janier J. Ram?rez Landaburo 
Facultad - 6 
Tel-837-3121 
http://www.uci.cu



From biojava at hannes.oib.com  Thu May 16 18:45:48 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 16 May 2013 20:45:48 +0200
Subject: [Biojava-l] help with fastq
In-Reply-To: <0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>
References: <23602a14-84c7-4b34-ad02-9a6d64f8d50d@ucimail4.uci.cu>
	<0db2f952-6db0-44ba-9cdb-c006b0a5a71a@ucimail4.uci.cu>
Message-ID: <CAPXi2mmtv7Tpdj4FHCKnzCiRFho6x+zzERM3EKxOtdixX5f-8Q@mail.gmail.com>

Can you show some code, so we can see where the problem is?


On Thu, May 16, 2013 at 3:51 PM, Janier J. Ram?rez <
jjramirez at estudiantes.uci.cu> wrote:

> Hi again comunity !
>
> I need this time generate a Fastq file from many fasta files, using
> illumina scores (one default value).
> I ?ve tried this but am having a problem wthis the header and the
> identifier of the file.
> makes Biojava this work ?
>
> greetings
>
> Janier
> --
>
>
> Universidad de las Ciencias Inform?ticas
> Janier J. Ram?rez Landaburo
> Facultad - 6
> Tel-837-3121
> http://www.uci.cu
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From bbimber at gmail.com  Thu May 23 18:53:48 2013
From: bbimber at gmail.com (Ben Bimber)
Date: Thu, 23 May 2013 11:53:48 -0700
Subject: [Biojava-l] reading genbank data
Message-ID: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>

Hello,

To date, I have used BioJava3 for very limited work such as read/writing
FASTA files.  I am trying to determine the best method to read and parse
sequence in genbank format using java.  As far as i can tell, legacy
BioJava has classes to support this (RichSequence.IOTools); however, I do
not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
have support for parsing genbank files?

Thanks in advance for any help.

-Ben


From biojava at hannes.oib.com  Thu May 23 20:14:39 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 23 May 2013 22:14:39 +0200
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
Message-ID: <CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>

Well, it doesn't look like that was ported to biojava 3 yet.

We'll add that to the todo list?


On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:

> Hello,
>
> To date, I have used BioJava3 for very limited work such as read/writing
> FASTA files.  I am trying to determine the best method to read and parse
> sequence in genbank format using java.  As far as i can tell, legacy
> BioJava has classes to support this (RichSequence.IOTools); however, I do
> not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
> have support for parsing genbank files?
>
> Thanks in advance for any help.
>
> -Ben
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From andreas at sdsc.edu  Fri May 24 05:36:10 2013
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 23 May 2013 22:36:10 -0700
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
	<CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
Message-ID: <CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>

Hi Hannes,

would you be interested in taking this one on?

Thanks,

Andreas


On Thu, May 23, 2013 at 1:14 PM, Hannes Brandst?tter-M?ller <
biojava at hannes.oib.com> wrote:

> Well, it doesn't look like that was ported to biojava 3 yet.
>
> We'll add that to the todo list?
>
>
> On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:
>
> > Hello,
> >
> > To date, I have used BioJava3 for very limited work such as read/writing
> > FASTA files.  I am trying to determine the best method to read and parse
> > sequence in genbank format using java.  As far as i can tell, legacy
> > BioJava has classes to support this (RichSequence.IOTools); however, I do
> > not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
> > have support for parsing genbank files?
> >
> > Thanks in advance for any help.
> >
> > -Ben
> > _______________________________________________
> > 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 biojava at hannes.oib.com  Fri May 24 07:09:05 2013
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 24 May 2013 09:09:05 +0200
Subject: [Biojava-l] reading genbank data
In-Reply-To: <CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>
References: <CAN+oBCtMN-BVJ=oKoMGLTRT0tTeabG+vo2CX5nHOiGf6bu9P8w@mail.gmail.com>
	<CAPXi2mnjnMMVCNFX6DwOwDk4xPXnuyAc+U1ZRYPU1iyQiGXO0w@mail.gmail.com>
	<CALthepyswX=-Sw1FhEELR8MEA69cAkmuNVSZXfvWv08pj=+weg@mail.gmail.com>
Message-ID: <CAPXi2mnt-u1V6uF_rT=kmYBA9ZG1GhJCFde1mrXjT+beT0_qkQ@mail.gmail.com>

I still need to finish up the last task (unfortunately I'm a bit short on
spare time currently) but I guess since it's parsing, I could work on
that...

Hannes


On Fri, May 24, 2013 at 7:36 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Hannes,
>
> would you be interested in taking this one on?
>
> Thanks,
>
> Andreas
>
>
> On Thu, May 23, 2013 at 1:14 PM, Hannes Brandst?tter-M?ller <
> biojava at hannes.oib.com> wrote:
>
>> Well, it doesn't look like that was ported to biojava 3 yet.
>>
>> We'll add that to the todo list?
>>
>>
>> On Thu, May 23, 2013 at 8:53 PM, Ben Bimber <bbimber at gmail.com> wrote:
>>
>> > Hello,
>> >
>> > To date, I have used BioJava3 for very limited work such as read/writing
>> > FASTA files.  I am trying to determine the best method to read and parse
>> > sequence in genbank format using java.  As far as i can tell, legacy
>> > BioJava has classes to support this (RichSequence.IOTools); however, I
>> do
>> > not see anything in BioJava3 related to parsing Genbank.  Does BioJava3
>> > have support for parsing genbank files?
>> >
>> > Thanks in advance for any help.
>> >
>> > -Ben
>> > _______________________________________________
>> > 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 sagayanilo at gmail.com  Wed May 29 11:52:51 2013
From: sagayanilo at gmail.com (Christina Nilofer)
Date: Wed, 29 May 2013 17:22:51 +0530
Subject: [Biojava-l] Regarding the transcription script
Message-ID: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>

Hi Sir,

This is christina,

In your code for transcription input was "atgccgaatcgtaa"
and the output was   "augccgaaucguaa".
 Here in this you have replaced t's with u's but the output must be
"uacggcuuagcauu"


we are not changing dna to rna, we are transcribing.

-- 
*Christy*
**
**


From amr_alhossary at hotmail.com  Wed May 29 12:00:06 2013
From: amr_alhossary at hotmail.com (Amr AL-HOSSARY)
Date: Wed, 29 May 2013 20:00:06 +0800
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
Message-ID: <BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>

Here is the definition of transcription from Wikipedia:

"Transcription is the first step of gene expression, in which a particular
segment of DNA is copied into RNA by the enzyme, RNA polymerase"


http://en.wikipedia.org/wiki/Transcription_(genetics)

Regards

Amr

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Christina Nilofer
Sent: Wednesday, May 29, 2013 7:53 PM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Regarding the transcription script

Hi Sir,

This is christina,

In your code for transcription input was "atgccgaatcgtaa"
and the output was   "augccgaaucguaa".
 Here in this you have replaced t's with u's but the output must be
"uacggcuuagcauu"


we are not changing dna to rna, we are transcribing.

--
*Christy*
**
**
_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l


From dasarnow at gmail.com  Wed May 29 17:42:44 2013
From: dasarnow at gmail.com (Daniel Asarnow)
Date: Wed, 29 May 2013 10:42:44 -0700
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
	<BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
Message-ID: <CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>

And the third sentence from that article is:  "during transcription, a DNA
sequence is read by an RNA polymerase, which produces a *complementary*,
antiparallel RNA strand."

mRNA is complementary to the *non-coding* strand. If the original sequence
is coding, you just change T and U. If not, you must make a complement
containing U.

The example sequence is clearly coding, thus the confusion.

-da


On Wed, May 29, 2013 at 5:00 AM, Amr AL-HOSSARY
<amr_alhossary at hotmail.com>wrote:

> Here is the definition of transcription from Wikipedia:
>
> "Transcription is the first step of gene expression, in which a particular
> segment of DNA is copied into RNA by the enzyme, RNA polymerase"
>
>
> http://en.wikipedia.org/wiki/Transcription_(genetics)
>
> Regards
>
> Amr
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Christina
> Nilofer
> Sent: Wednesday, May 29, 2013 7:53 PM
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Regarding the transcription script
>
> Hi Sir,
>
> This is christina,
>
> In your code for transcription input was "atgccgaatcgtaa"
> and the output was   "augccgaaucguaa".
>  Here in this you have replaced t's with u's but the output must be
> "uacggcuuagcauu"
>
>
> we are not changing dna to rna, we are transcribing.
>
> --
> *Christy*
> **
> **
> _______________________________________________
> 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 p.j.a.cock at googlemail.com  Wed May 29 18:44:10 2013
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 29 May 2013 19:44:10 +0100
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
	<BLU404-EAS178B2A5958D252159DE20A18E900@phx.gbl>
	<CANBcHWoVaLGhZ_QY2AhfpzULk541v1fr9iSNuX0JoL2jCiRZbA@mail.gmail.com>
Message-ID: <CAKVJ-_53hbNQibd5DhbC69p1Y2Rk8HjmQCUycRaN40yBSsw1_Q@mail.gmail.com>

On Wed, May 29, 2013 at 6:42 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> And the third sentence from that article is:  "during transcription, a DNA
> sequence is read by an RNA polymerase, which produces a *complementary*,
> antiparallel RNA strand."
>
> mRNA is complementary to the *non-coding* strand. If the original sequence
> is coding, you just change T and U. If not, you must make a complement
> containing U.
>
> The example sequence is clearly coding, thus the confusion.
>
> -da

Hi Christina and all,

This has come up on the Biopython mailing list a few times too.
Does the strand section in the Biopython tutorial help at all?

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc24

"Before talking about transcription, I want to try and clarify the
strand issue. Consider the following (made up) stretch of double
stranded DNA which encodes a short peptide: ...
The actual biological transcription process works from the
template strand, doing a reverse complement (TCAG -> CUGA)
to give the mRNA. However, in Biopython and bioinformatics
in general, we typically work directly with the coding strand
because this means we can get the mRNA sequence just
by switching T -> U."

Regards,

Peter


From sagayanilo at gmail.com  Thu May 30 03:39:08 2013
From: sagayanilo at gmail.com (Christina Nilofer)
Date: Thu, 30 May 2013 09:09:08 +0530
Subject: [Biojava-l] Regarding the transcription script
In-Reply-To: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
References: <CAOU5aeq2Sg_DAMX32VOrpsoNZ1+SC=wkDZDj1zESbkfbPjE--A@mail.gmail.com>
Message-ID: <CAOU5aeoCP_=rvrWo3ir36R+LreB7KDWAeoT7+6rCCdnfssgbNg@mail.gmail.com>

Thank you for the reply sir, now I am able to understand the concept
better, thank you sirs.

On Wed, May 29, 2013 at 5:22 PM, Christina Nilofer <sagayanilo at gmail.com>wrote:

> Hi Sir,
>
> This is christina,
>
> In your code for transcription input was "atgccgaatcgtaa"
> and the output was   "augccgaaucguaa".
>  Here in this you have replaced t's with u's but the output must be
> "uacggcuuagcauu"
>
>
> we are not changing dna to rna, we are transcribing.
>
> --
> *Christy*
> **
> **
>
>



-- 
*Christy*
**
**