From andreas.prlic at gmail.com  Tue Nov  1 18:55:08 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Tue, 1 Nov 2011 15:55:08 -0700
Subject: [Biojava-l] queries on biojava
In-Reply-To: <1319952341.16116.YahooMailNeo@web112102.mail.gq1.yahoo.com>
References: <1319952341.16116.YahooMailNeo@web112102.mail.gq1.yahoo.com>
Message-ID: <CALthepzs0WTuhJm70bD9zLPBxdZ3pmLx+8hQPsaM8-kY-Nk7nA@mail.gmail.com>

Hi Parinita,

Please don't send BioJava related questions to me directly, but to the
mailing list.

Probably your genome sequences are very long and require a lot of
memory? Try increasing your Java memory to the maximum available on
your computer with something like -Xmx4G .

If this does not help and your DNA sequences are too long, you might
have to use either shorter DNA sequences, or you use one of the
alignment algorithms that are available for the alignment of larger
genomes.  Eg. Mummer might be one of the options.

Andreas


On Sat, Oct 29, 2011 at 10:25 PM, parinita ujoodha
<pari_ujoodha at yahoo.com> wrote:
> Hello andreas,
> ??? ??? ??? ??? ??? I am currently an undergraduate final year student on
> the computer science course at the university of Mauritius.? I am doing a
> project on a genome comparison tool and using java and biojava as
> programming tools.? I have certain queries and hope you can answer them.
> I have tried the MSA in the cookbook and it works fine but when I try to
> align genomes, the program crashes.
> I would sincerely like to know whether there is a way of? aligning genomes
> and displaying them in a pleasant interface
> I thank you in advance
>
> Regards
> Parinita
>
>
>


From andreas at sdsc.edu  Tue Nov  1 19:19:17 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 1 Nov 2011 16:19:17 -0700
Subject: [Biojava-l] [Biojava-dev] Genbank import
In-Reply-To: <F7848DBC-973A-4286-B662-FCEC9FBEABC3@charter.net>
References: <F7848DBC-973A-4286-B662-FCEC9FBEABC3@charter.net>
Message-ID: <CALthepwWaNavngzLciPR_KPpo-uGKvV++BTTbU4r_tnhYpvn2g@mail.gmail.com>

Hi Ed,

Interesting that you found this, this ancient tutorial has not been
modified since the early 2000s and has been replaced with the Cookbook
pages:

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

Some of the code for this is available as part of the BioJava-legacy
(v 1.8) project.

BioJava3 currently does not have a Genbank parser yet, only fasta. I
added it to the (new) missing features page :

http://www.biojava.org/wiki/BioJava3_Feature_Requests

Andreas



On Sun, Oct 30, 2011 at 7:54 PM, Ed Beaty <edbeaty at charter.net> wrote:
> Hello all. ?Is it possible to import Genbank (*.gb) format files using BioJava 3? ?I can't find the SeqIOTools class described in the GeneralReader example in the http://www.biojava.org/docs/bj_in_anger/ReadingGES.htm doc.
> Thanks,
> Ed Beaty
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


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Subject: [Biojava-l] Invitation to connect on LinkedIn
Message-ID: <1927181069.419433.1320202674916.JavaMail.app@ela4-bed82.prod>

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From biojava at hannes.oib.com  Thu Nov  3 09:08:22 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 3 Nov 2011 14:08:22 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
Message-ID: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>

Hi!

Is there a Class/Method in Biojava that calculates the Levenshtein
distance between two sequences? I could not find anything in the docs
at first search.

I need to compare 2 DNASequences (or Strings) and get the number of
insertions, deletions, and substitutions. Ideally, there would be an
option to abort the comparison if the number of mismatches exceeds a
certain number.

Hannes

From biojava at hannes.oib.com  Thu Nov  3 10:17:05 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 3 Nov 2011 15:17:05 +0100
Subject: [Biojava-l] Sequence Alignment and IUB Codes
Message-ID: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>

Does the biojava sequence alignment support IUB Codes?
http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation

Hannes

From andreas at sdsc.edu  Fri Nov  4 02:18:12 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 3 Nov 2011 23:18:12 -0700
Subject: [Biojava-l] Sequence Alignment and IUB Codes
In-Reply-To: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
References: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
Message-ID: <CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>

Hi Hannes,

I think that depends which substitution matrix you are using. Some of
them don't support ambiguity codes.

Andreas

On Thu, Nov 3, 2011 at 7:17 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Does the biojava sequence alignment support IUB Codes?
> http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation
>
> Hannes
> _______________________________________________
> 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 Nov  4 02:20:53 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 4 Nov 2011 07:20:53 +0100
Subject: [Biojava-l] Sequence Alignment and IUB Codes
In-Reply-To: <CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>
References: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
	<CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>
Message-ID: <CAPXi2mnR=4H3ZOHP=iPPPSZ16CAm+dnvxX6Ak1=30oF7V-i+kQ@mail.gmail.com>

Thanks Andreas, of course, that's where I can configure it. Thanks for
the clarification.
Hannes

On Fri, Nov 4, 2011 at 07:18, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes,
>
> I think that depends which substitution matrix you are using. Some of
> them don't support ambiguity codes.
>
> Andreas
>
> On Thu, Nov 3, 2011 at 7:17 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Does the biojava sequence alignment support IUB Codes?
>> http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation
>>
>> Hannes
>> _______________________________________________
>> 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 Nov  4 02:21:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 3 Nov 2011 23:21:57 -0700
Subject: [Biojava-l] BioJava in education
Message-ID: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>

Hi,

Is anybody using BioJava in teaching, or has been introduced to
BioJava as part of a course?

Andreas

From cfriedline at vcu.edu  Fri Nov  4 09:50:52 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Fri, 4 Nov 2011 09:50:52 -0400
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>

Andreas, 

I had to come to it on my own.  Seems the focus at this university is on Perl only and there's a serious (IMO) disconnect with our CS department.  Java (or some other OO language) is only a minor requirement for bioinformatics undergrads/graduate students.  However, I'd love to see this change and/or be involved in the development of a course to do just that.  We've been kicking around developing some intersession modules around dealing with genetic data sets using Java/BioJava, but doing actual research continues to stand in our way.

On a side note, have you seen the Java Evolutionary Biology Library?  Would be excellent to combine forces of these development efforts since JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely from a selfish user perspective.  ;-)

Chris

On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:

> Hi,
> 
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
> 
> Andreas
> _______________________________________________
> 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 Nov  4 19:11:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Nov 2011 16:11:46 -0700
Subject: [Biojava-l] BioJava in education
In-Reply-To: <B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
Message-ID: <CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>

Hi,

to quickly follow up: A few people have contacted me off list that
they were introduced to BioJava through some course. Interestingly no
teachers though who arranged this. I would be interested in organising
the exchange of teaching materials. If anybody wants to exchange power
points, homework assignment ideas, etc.  please let me know.


Chris wrote:
> On a side note, have you seen the Java Evolutionary Biology Library? ?Would be excellent to combine forces of these development efforts since JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely from a selfish user perspective. ?;-)

That is a great suggestion. Seems that project does not really have a
web presence. Any idea how to contact the main developers? There is no
mailing list. I guess one could try via sourceforge somehow.

Andreas




> Chris
>
> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>
>> Hi,
>>
>> Is anybody using BioJava in teaching, or has been introduced to
>> BioJava as part of a course?
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>


From simon.rayner.cn at gmail.com  Fri Nov  4 19:18:33 2011
From: simon.rayner.cn at gmail.com (simon rayner)
Date: Sat, 5 Nov 2011 07:18:33 +0800
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
Message-ID: <CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>

i've been trying to use biojava as a segment of an advanced bioinformatics
course for masters students but these are students who are studying
virology with a specific interest in bioinformatics.  Nevertheless, some
students take to it very easily but, for me, it seems the major drawback
with biojava is it is a lot more disjointed compared to bioperl,. By this i
mean, it's not always easy to find the classes you need, or if the class is
available, it was broken during a previous release, or simply wasn't
included in the latest version. I think biojava is the way to go for
training and a course development project might be the way to get a more
cohesive documentation set.

On Fri, Nov 4, 2011 at 9:50 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>
>> Andreas,
>>
>> I had to come to it on my own.  Seems the focus at this university is on
>> Perl only and there's a serious (IMO) disconnect with our CS department.
>>  Java (or some other OO language) is only a minor requirement for
>> bioinformatics undergrads/graduate students.  However, I'd love to see this
>> change and/or be involved in the development of a course to do just that.
>>  We've been kicking around developing some intersession modules around
>> dealing with genetic data sets using Java/BioJava, but doing actual
>> research continues to stand in our way.
>>
>> On a side note, have you seen the Java Evolutionary Biology Library?
>>  Would be excellent to combine forces of these development efforts since
>> JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely
>> from a selfish user perspective.  ;-)
>>
>> Chris
>>
>> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>>
>> > Hi,
>> >
>> > Is anybody using BioJava in teaching, or has been introduced to
>> > BioJava as part of a course?
>> >
>> > Andreas
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895 (office)
> +86 18627113001 (cell)
>
>


-- 
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

+86 (27) 87199895 (office)
+86 18627113001 (cell)

From andreas at sdsc.edu  Fri Nov  4 20:37:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Nov 2011 17:37:03 -0700
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
	<CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>
Message-ID: <CALthepwgcRJs+1dsyCLGhG-ovvwf1kLUdYpYcO_j5JVqxhbQMA@mail.gmail.com>

Thanks Simon, v. interesting. Can you provide some more details? What
kind of tasks were you requiring the students to perform? I agree, a
project to prepare course material would be great.

Andreas

On Fri, Nov 4, 2011 at 4:18 PM, simon rayner <simon.rayner.cn at gmail.com> wrote:
> i've been trying to use biojava as a segment of an advanced bioinformatics
> course for masters students but these are students who are studying
> virology with a specific interest in bioinformatics. ?Nevertheless, some
> students take to it very easily but, for me, it seems the major drawback
> with biojava is it is a lot more disjointed compared to bioperl,. By this i
> mean, it's not always easy to find the classes you need, or if the class is
> available, it was broken during a previous release, or simply wasn't
> included in the latest version. I think biojava is the way to go for
> training and a course development project might be the way to get a more
> cohesive documentation set.
>
> On Fri, Nov 4, 2011 at 9:50 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>>
>>> Andreas,
>>>
>>> I had to come to it on my own. ?Seems the focus at this university is on
>>> Perl only and there's a serious (IMO) disconnect with our CS department.
>>> ?Java (or some other OO language) is only a minor requirement for
>>> bioinformatics undergrads/graduate students. ?However, I'd love to see this
>>> change and/or be involved in the development of a course to do just that.
>>> ?We've been kicking around developing some intersession modules around
>>> dealing with genetic data sets using Java/BioJava, but doing actual
>>> research continues to stand in our way.
>>>
>>> On a side note, have you seen the Java Evolutionary Biology Library?
>>> ?Would be excellent to combine forces of these development efforts since
>>> JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely
>>> from a selfish user perspective. ?;-)
>>>
>>> Chris
>>>
>>> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>>>
>>> > Hi,
>>> >
>>> > Is anybody using BioJava in teaching, or has been introduced to
>>> > BioJava as part of a course?
>>> >
>>> > Andreas
>>> > _______________________________________________
>>> > 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
>>>
>>
>>
>>
>> --
>> Simon Rayner
>>
>> State Key Laboratory of Virology
>> Wuhan Institute of Virology
>> Chinese Academy of Sciences
>> Wuhan, Hubei 430071
>> P.R.China
>>
>> +86 (27) 87199895 (office)
>> +86 18627113001 (cell)
>>
>>
>
>
> --
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895?(office)
> +86 18627113001?(cell)
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From cfriedline at vcu.edu  Sat Nov  5 10:18:18 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Sat, 5 Nov 2011 10:18:18 -0400
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>
Message-ID: <9B411F3A-FCC2-449A-9F3C-44AD91DF30BD@vcu.edu>


On Nov 4, 2011, at 7:11 PM, Andreas Prlic wrote:

> 
> That is a great suggestion. Seems that project does not really have a
> web presence. Any idea how to contact the main developers? There is no
> mailing list. I guess one could try via sourceforge somehow.

You may want to contact either Alexei Drummond (http://compevol.auckland.ac.nz/people/)
or Andrew Rambaut (http://tree.bio.ed.ac.uk/).  I think their emails are on their respective sites.

Chris 

From biojava at hannes.oib.com  Mon Nov  7 08:39:16 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Mon, 7 Nov 2011 14:39:16 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
Message-ID: <CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>

Following up:

If there is no such thing, should I make it available if I write it?

Hannes

On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi!
>
> Is there a Class/Method in Biojava that calculates the Levenshtein
> distance between two sequences? I could not find anything in the docs
> at first search.
>
> I need to compare 2 DNASequences (or Strings) and get the number of
> insertions, deletions, and substitutions. Ideally, there would be an
> option to abort the comparison if the number of mismatches exceeds a
> certain number.
>
> Hannes
>


From andreas at sdsc.edu  Mon Nov  7 09:42:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 7 Nov 2011 06:42:57 -0800
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
Message-ID: <CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>

Hi Hannes,

you are right, this does not exist yet. Somebody else asked the same
question a few weeks ago. As such it would be great if you could
provide a patch, there might be other people interested in that, too.

Andreas

On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Following up:
>
> If there is no such thing, should I make it available if I write it?
>
> Hannes
>
> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Hi!
>>
>> Is there a Class/Method in Biojava that calculates the Levenshtein
>> distance between two sequences? I could not find anything in the docs
>> at first search.
>>
>> I need to compare 2 DNASequences (or Strings) and get the number of
>> insertions, deletions, and substitutions. Ideally, there would be an
>> option to abort the comparison if the number of mismatches exceeds a
>> certain number.
>>
>> Hannes
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From forumjspro at gmail.com  Mon Nov  7 10:03:55 2011
From: forumjspro at gmail.com (forumjspro at gmail.com)
Date: Mon, 7 Nov 2011 16:03:55 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
Message-ID: <6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>

Hi Hannes,

You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors. 

But it will not stop when a maximal number of errors is reached ...

JS

Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :

> Hi Hannes,
> 
> you are right, this does not exist yet. Somebody else asked the same
> question a few weeks ago. As such it would be great if you could
> provide a patch, there might be other people interested in that, too.
> 
> Andreas
> 
> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Following up:
>> 
>> If there is no such thing, should I make it available if I write it?
>> 
>> Hannes
>> 
>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi!
>>> 
>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>> distance between two sequences? I could not find anything in the docs
>>> at first search.
>>> 
>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>> insertions, deletions, and substitutions. Ideally, there would be an
>>> option to abort the comparison if the number of mismatches exceeds a
>>> certain number.
>>> 
>>> Hannes
>>> 
>> 
>> _______________________________________________
>> 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 cfriedline at vcu.edu  Mon Nov  7 10:58:28 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 7 Nov 2011 10:58:28 -0500
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
Message-ID: <7E0C3BDA-03F4-4723-BE91-0F4B274DD671@vcu.edu>

Hannes,

If you really want to use Levenstein distance, there's a method in Apache commons lang StringUtils.

Chris

On Nov 3, 2011, at 9:08 AM, Hannes Brandst?tter-M?ller wrote:

> Hi!
> 
> Is there a Class/Method in Biojava that calculates the Levenshtein
> distance between two sequences? I could not find anything in the docs
> at first search.
> 
> I need to compare 2 DNASequences (or Strings) and get the number of
> insertions, deletions, and substitutions. Ideally, there would be an
> option to abort the comparison if the number of mismatches exceeds a
> certain number.
> 
> Hannes
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l



From amr_alhossary at hotmail.com  Mon Nov  7 09:48:28 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Mon, 7 Nov 2011 16:48:28 +0200
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <BLU150-ds1385430025799F5590E8428ED90@phx.gbl>

Sorry for the late reply.
Although I come into it on my own, I had the interest to voluntarily teach 
it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
I focused on BioJava 1.7 and I May send you the presentation if you like.
Unfortunately, this department was closed after 2 successive intakes, so I 
didn't update it.


Amr

--------------------------------------------------
From: "Andreas Prlic" <andreas at sdsc.edu>
Sent: Friday, November 04, 2011 8:21 AM
To: "Biojava" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] BioJava in education

> Hi,
>
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

From amr_alhossary at hotmail.com  Mon Nov  7 09:48:28 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Mon, 7 Nov 2011 16:48:28 +0200
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>

Sorry for the late reply.
Although I come into it on my own, I had the interest to voluntarily teach 
it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
I focused on BioJava 1.7 and I May send you the presentation if you like.
Unfortunately, this department was closed after 2 successive intakes, so I 
didn't update it.


Amr

--------------------------------------------------
From: "Andreas Prlic" <andreas at sdsc.edu>
Sent: Friday, November 04, 2011 8:21 AM
To: "Biojava" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] BioJava in education

> Hi,
>
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
>
> Andreas
> _______________________________________________
> 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  Wed Nov  9 04:01:15 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 9 Nov 2011 10:01:15 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
Message-ID: <CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>

Thanks.

I am thinking about implementing a modified MatrixAligner to fit my
needs here. Direct Levenstein Distance is not exactly right for my
application, because there are 0 to n insertions/deletions.

A direct LevensteinDistance as implemented in would not give me all
the Information I need.

Thanks for the hints and input.

Hannes

PS we seriously need more examples in the Cookbook - I'll submit some
later, but the modified N-W Aligner mentioned below would make a good
example too, don't you think? ;)

On Mon, Nov 7, 2011 at 16:03,  <forumjspro at gmail.com> wrote:
> Hi Hannes,
>
> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>
> But it will not stop when a maximal number of errors is reached ...
>
> JS
>
> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>
>> Hi Hannes,
>>
>> you are right, this does not exist yet. Somebody else asked the same
>> question a few weeks ago. As such it would be great if you could
>> provide a patch, there might be other people interested in that, too.
>>
>> Andreas
>>
>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Following up:
>>>
>>> If there is no such thing, should I make it available if I write it?
>>>
>>> Hannes
>>>
>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Hi!
>>>>
>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>> distance between two sequences? I could not find anything in the docs
>>>> at first search.
>>>>
>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>> option to abort the comparison if the number of mismatches exceeds a
>>>> certain number.
>>>>
>>>> Hannes
>>>>
>>>
>>> _______________________________________________
>>> 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 khalil.elmazouari at gmail.com  Mon Nov 14 11:00:37 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Mon, 14 Nov 2011 17:00:37 +0100
Subject: [Biojava-l] Rename RichSequence
Message-ID: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>

Hi,

how to rename a RichSequence?

Thanks


From Dietmar.Birzer at biologie.uni-regensburg.de  Mon Nov 14 11:53:29 2011
From: Dietmar.Birzer at biologie.uni-regensburg.de (Dietmar Birzer)
Date: Mon, 14 Nov 2011 17:53:29 +0100
Subject: [Biojava-l] Exception thrown when parsing GenBank file
Message-ID: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>


Hi all, 

I am currently trying to debug a little software application which uses BioJava's core-1.8.1.jar library because it has started to throw exceptions a while ago.  

I guess the problem is, that the GenbankLocationParser is not able to handle "Het" entries in the features section of the GenBank/GenPept format, e.g.  

 Het             join(bond(9),bond(125))  
                     /heterogen="( NA,   5 )"  

for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .  

Calling   

new GenpeptRichSequenceDB().getRichSequence("14719485");  

will result in an error message like:  

Error while querying 14719485!  
org.biojava.bio.BioException: Failed to read Genbank sequence  
at org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:158)  
Caused by: org.biojava.bio.BioException: Could not read sequence  
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)  
at org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:154)  
... 2 more  
Caused by: org.biojava.bio.seq.io.ParseException: Could not understand position: bond(9  
at org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:286)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:272)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:237)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:132)  
at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:508)  
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)  
... 3 more  

I have checked several other database entires and none of the ones that worked had a "Het" entry. But I also failed at 56965892, 13786715, 209156668 and 12084365. Has anybody else come across this problem or knows how to fix it?  

Thanks,  
 Dietmar


From p.j.a.cock at googlemail.com  Mon Nov 14 12:29:31 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 14 Nov 2011 17:29:31 +0000
Subject: [Biojava-l] Exception thrown when parsing GenBank file
In-Reply-To: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
Message-ID: <CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>

On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>
> Hi all,
>
> I am currently trying to debug a little software application which
> uses BioJava's core-1.8.1.jar library because it has started to
> throw exceptions a while ago.
>
> I guess the problem is, that the GenbankLocationParser is not
> able to handle "Het" entries in the features section of the
> GenBank/GenPept format, e.g.
>
> ?Het ? ? ? ? ? ? join(bond(9),bond(125))
> ? ? ? ? ? ? ? ? ? ? /heterogen="( NA, ? 5 )"
>
> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .

Interesting - note the bond locations are not in the official
DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
that seems to be intended only for nucleotides and not proteins as here.
It might be worth contacting the NCBI to find out if there is an official
specification covering these location strings?

Peter


From gwaldon at geneinfinity.org  Mon Nov 14 18:20:02 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 14 Nov 2011 17:20:02 -0600
Subject: [Biojava-l] Rename RichSequence
In-Reply-To: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>
References: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>
Message-ID: <20111114172002.19321y9clytb4ug0@gator1273.hostgator.com>

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

> Hi,
>
> how to rename a RichSequence?
>
> Thanks
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

Hi,

You cannot rename SimpleRichSequence by design. A simple way is to  
wrap the sequence in your own implementation of RichSequence and  
delegate to it.

Regards,
George


From biojava at hannes.oib.com  Tue Nov 15 09:10:43 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Tue, 15 Nov 2011 15:10:43 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
	<CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
Message-ID: <CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>

Well, I have implemented a first version that is running quite well
for me and my needs/specifications, although I did not integrate it
directly into the biojava class hierarchy yet.
Is anyone interested in taking a look at it and giving me some
feedback if I shoud invest the time and work to make it includable
into biojava?

Hannes

On Wed, Nov 9, 2011 at 10:01, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Thanks.
>
> I am thinking about implementing a modified MatrixAligner to fit my
> needs here. Direct Levenstein Distance is not exactly right for my
> application, because there are 0 to n insertions/deletions.
>
> A direct LevensteinDistance as implemented in would not give me all
> the Information I need.
>
> Thanks for the hints and input.
>
> Hannes
>
> PS we seriously need more examples in the Cookbook - I'll submit some
> later, but the modified N-W Aligner mentioned below would make a good
> example too, don't you think? ;)
>
> On Mon, Nov 7, 2011 at 16:03, ?<forumjspro at gmail.com> wrote:
>> Hi Hannes,
>>
>> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>>
>> But it will not stop when a maximal number of errors is reached ...
>>
>> JS
>>
>> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>>
>>> Hi Hannes,
>>>
>>> you are right, this does not exist yet. Somebody else asked the same
>>> question a few weeks ago. As such it would be great if you could
>>> provide a patch, there might be other people interested in that, too.
>>>
>>> Andreas
>>>
>>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Following up:
>>>>
>>>> If there is no such thing, should I make it available if I write it?
>>>>
>>>> Hannes
>>>>
>>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Hi!
>>>>>
>>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>>> distance between two sequences? I could not find anything in the docs
>>>>> at first search.
>>>>>
>>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>>> option to abort the comparison if the number of mismatches exceeds a
>>>>> certain number.
>>>>>
>>>>> Hannes
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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 andreas at sdsc.edu  Tue Nov 15 10:53:50 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 15 Nov 2011 07:53:50 -0800
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
	<CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
	<CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>
Message-ID: <CALthepz=w8z73=yGSqX+GM-q-nwJSdRd+kokE8EHZUL3GgJWpw@mail.gmail.com>

you could send it to the list here and ask for feedback..

Andreas

On Tue, Nov 15, 2011 at 6:10 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Well, I have implemented a first version that is running quite well
> for me and my needs/specifications, although I did not integrate it
> directly into the biojava class hierarchy yet.
> Is anyone interested in taking a look at it and giving me some
> feedback if I shoud invest the time and work to make it includable
> into biojava?
>
> Hannes
>
> On Wed, Nov 9, 2011 at 10:01, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Thanks.
>>
>> I am thinking about implementing a modified MatrixAligner to fit my
>> needs here. Direct Levenstein Distance is not exactly right for my
>> application, because there are 0 to n insertions/deletions.
>>
>> A direct LevensteinDistance as implemented in would not give me all
>> the Information I need.
>>
>> Thanks for the hints and input.
>>
>> Hannes
>>
>> PS we seriously need more examples in the Cookbook - I'll submit some
>> later, but the modified N-W Aligner mentioned below would make a good
>> example too, don't you think? ;)
>>
>> On Mon, Nov 7, 2011 at 16:03, ?<forumjspro at gmail.com> wrote:
>>> Hi Hannes,
>>>
>>> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>>>
>>> But it will not stop when a maximal number of errors is reached ...
>>>
>>> JS
>>>
>>> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>>>
>>>> Hi Hannes,
>>>>
>>>> you are right, this does not exist yet. Somebody else asked the same
>>>> question a few weeks ago. As such it would be great if you could
>>>> provide a patch, there might be other people interested in that, too.
>>>>
>>>> Andreas
>>>>
>>>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Following up:
>>>>>
>>>>> If there is no such thing, should I make it available if I write it?
>>>>>
>>>>> Hannes
>>>>>
>>>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>>>> <biojava at hannes.oib.com> wrote:
>>>>>> Hi!
>>>>>>
>>>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>>>> distance between two sequences? I could not find anything in the docs
>>>>>> at first search.
>>>>>>
>>>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>>>> option to abort the comparison if the number of mismatches exceeds a
>>>>>> certain number.
>>>>>>
>>>>>> Hannes
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>>
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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


From lfrohman at gmail.com  Wed Nov 16 11:14:18 2011
From: lfrohman at gmail.com (Lance Frohman)
Date: Wed, 16 Nov 2011 08:14:18 -0800
Subject: [Biojava-l] biojava-ensembl
Message-ID: <CAOseA7ww6OoX50Ha2UwqP-6cJ_-PLb9vGaCkghrV0eqb_H2hag@mail.gmail.com>

Where do I find the source code for biojava-ensembl?

thanks

From Dietmar.Birzer at biologie.uni-regensburg.de  Wed Nov 23 10:18:29 2011
From: Dietmar.Birzer at biologie.uni-regensburg.de (Dietmar Birzer)
Date: Wed, 23 Nov 2011 16:18:29 +0100
Subject: [Biojava-l] Antw: Re:  Exception thrown when parsing GenBank file
In-Reply-To: <CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
Message-ID: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>

 Hi all,

as the GenbankLocationParser from biojava-1.8.1 is not working properly anymore, I was wondering if there is an equivalent way to do this ( GenpeptRichSequenceDB().getRichSequence("14719485") ) using BioJava 3.
Unfortunately I could not find any GenBank/GenPept parser so far. Is that because it does not exist (yet), or just because I have not looked properly?

Best wishes
 Dietmar
 
>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>> 
On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>
> Hi all,
>
> I am currently trying to debug a little software application which
> uses BioJava's core-1.8.1.jar library because it has started to
> throw exceptions a while ago.
>
> I guess the problem is, that the GenbankLocationParser is not
> able to handle "Het" entries in the features section of the
> GenBank/GenPept format, e.g.
>
>  Het             join(bond(9),bond(125))
>                     /heterogen="( NA,   5 )"
>
> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .

Interesting - note the bond locations are not in the official
DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
that seems to be intended only for nucleotides and not proteins as here.
It might be worth contacting the NCBI to find out if there is an official
specification covering these location strings?

Peter




From andreas at sdsc.edu  Wed Nov 23 10:34:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 23 Nov 2011 07:34:46 -0800
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
Message-ID: <CALthepxMGfTsFH8UyHJ2==wUqbXpBJXmLNjrY2HTqOsga_Ro=w@mail.gmail.com>

Hi Dietmar,

The genbank parser is on top of the feature request list for biojava
3: http://biojava.org/wiki/BioJava3_Feature_Requests

Anybody who wants to take an initiative here and claim ownership of
this topic is welcome...

Andreas


On Wed, Nov 23, 2011 at 7:18 AM, Dietmar Birzer
<Dietmar.Birzer at biologie.uni-regensburg.de> wrote:
> ?Hi all,
>
> as the GenbankLocationParser from biojava-1.8.1 is not working properly anymore, I was wondering if there is an equivalent way to do this ( GenpeptRichSequenceDB().getRichSequence("14719485") ) using BioJava 3.
> Unfortunately I could not find any GenBank/GenPept parser so far. Is that because it does not exist (yet), or just because I have not looked properly?
>
> Best wishes
> ?Dietmar
>
>>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>>
> On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>>
>> Hi all,
>>
>> I am currently trying to debug a little software application which
>> uses BioJava's core-1.8.1.jar library because it has started to
>> throw exceptions a while ago.
>>
>> I guess the problem is, that the GenbankLocationParser is not
>> able to handle "Het" entries in the features section of the
>> GenBank/GenPept format, e.g.
>>
>> ?Het ? ? ? ? ? ? join(bond(9),bond(125))
>> ? ? ? ? ? ? ? ? ? ? /heterogen="( NA, ? 5 )"
>>
>> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
>
> Interesting - note the bond locations are not in the official
> DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
>
> However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
> that seems to be intended only for nucleotides and not proteins as here.
> It might be worth contacting the NCBI to find out if there is an official
> specification covering these location strings?
>
> Peter
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>


From gwaldon at geneinfinity.org  Wed Nov 23 11:06:57 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Wed, 23 Nov 2011 10:06:57 -0600
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
Message-ID: <20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>

Hi Dietmar,

The GenbankLocationParser from biojava-1.8.1 is working perfectly as  
long as you feed him with DNA locations that use the syntax described  
in the DDBJ/EMBL/GenBank feature table definition. What you've got  
(join(bond(9),bond(125))...) is a pseudo GenBank format that  
apparently describes protein structure and uses a slightly different  
syntax to indicate heteroatom locations. That is why you get all these  
exceptions thrown.

George



Quoting Dietmar Birzer <Dietmar.Birzer at biologie.uni-regensburg.de>:

>  Hi all,
>
> as the GenbankLocationParser from biojava-1.8.1 is not working  
> properly anymore, I was wondering if there is an equivalent way to  
> do this ( GenpeptRichSequenceDB().getRichSequence("14719485") )  
> using BioJava 3.
> Unfortunately I could not find any GenBank/GenPept parser so far. Is  
> that because it does not exist (yet), or just because I have not  
> looked properly?
>
> Best wishes
>  Dietmar
>
>>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>>
> On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>>
>> Hi all,
>>
>> I am currently trying to debug a little software application which
>> uses BioJava's core-1.8.1.jar library because it has started to
>> throw exceptions a while ago.
>>
>> I guess the problem is, that the GenbankLocationParser is not
>> able to handle "Het" entries in the features section of the
>> GenBank/GenPept format, e.g.
>>
>>  Het             join(bond(9),bond(125))
>>                     /heterogen="( NA,   5 )"
>>
>> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
>
> Interesting - note the bond locations are not in the official
> DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
>
> However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
> that seems to be intended only for nucleotides and not proteins as here.
> It might be worth contacting the NCBI to find out if there is an official
> specification covering these location strings?
>
> Peter
>
>
>
> _______________________________________________
> 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 Nov 23 12:01:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Nov 2011 17:01:11 +0000
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
	<20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>
Message-ID: <CAKVJ-_49aO3P=GE6i+ULu_fSEw3LoA8v+1M3O5d9kG0wTxF0ag@mail.gmail.com>

On Wed, Nov 23, 2011 at 4:06 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Hi Dietmar,
>
> The GenbankLocationParser from biojava-1.8.1 is working perfectly as long as
> you feed him with DNA locations that use the syntax described in the
> DDBJ/EMBL/GenBank feature table definition.

As mentioned earlier, that document only covers nucleotide sequences,
not proteins as used in GenPept and the EMBL patents database:
http://lists.open-bio.org/pipermail/biojava-l/2011-November/007889.html

> What you've got (join(bond(9),bond(125))...) is a pseudo GenBank format
> that apparently describes protein structure and uses a slightly different
> syntax to indicate heteroatom locations. That is why you get all these
> exceptions thrown.
>
> George

It would be interesting to see if the EBI offer the same record(s) in
EMBL format, and if that too uses the (undocumented?) bond locations.

Peter

From andreas.prlic at gmail.com  Tue Nov  1 22:55:08 2011
From: andreas.prlic at gmail.com (Andreas Prlic)
Date: Tue, 1 Nov 2011 15:55:08 -0700
Subject: [Biojava-l] queries on biojava
In-Reply-To: <1319952341.16116.YahooMailNeo@web112102.mail.gq1.yahoo.com>
References: <1319952341.16116.YahooMailNeo@web112102.mail.gq1.yahoo.com>
Message-ID: <CALthepzs0WTuhJm70bD9zLPBxdZ3pmLx+8hQPsaM8-kY-Nk7nA@mail.gmail.com>

Hi Parinita,

Please don't send BioJava related questions to me directly, but to the
mailing list.

Probably your genome sequences are very long and require a lot of
memory? Try increasing your Java memory to the maximum available on
your computer with something like -Xmx4G .

If this does not help and your DNA sequences are too long, you might
have to use either shorter DNA sequences, or you use one of the
alignment algorithms that are available for the alignment of larger
genomes.  Eg. Mummer might be one of the options.

Andreas


On Sat, Oct 29, 2011 at 10:25 PM, parinita ujoodha
<pari_ujoodha at yahoo.com> wrote:
> Hello andreas,
> ??? ??? ??? ??? ??? I am currently an undergraduate final year student on
> the computer science course at the university of Mauritius.? I am doing a
> project on a genome comparison tool and using java and biojava as
> programming tools.? I have certain queries and hope you can answer them.
> I have tried the MSA in the cookbook and it works fine but when I try to
> align genomes, the program crashes.
> I would sincerely like to know whether there is a way of? aligning genomes
> and displaying them in a pleasant interface
> I thank you in advance
>
> Regards
> Parinita
>
>
>



From andreas at sdsc.edu  Tue Nov  1 23:19:17 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 1 Nov 2011 16:19:17 -0700
Subject: [Biojava-l] [Biojava-dev] Genbank import
In-Reply-To: <F7848DBC-973A-4286-B662-FCEC9FBEABC3@charter.net>
References: <F7848DBC-973A-4286-B662-FCEC9FBEABC3@charter.net>
Message-ID: <CALthepwWaNavngzLciPR_KPpo-uGKvV++BTTbU4r_tnhYpvn2g@mail.gmail.com>

Hi Ed,

Interesting that you found this, this ancient tutorial has not been
modified since the early 2000s and has been replaced with the Cookbook
pages:

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

Some of the code for this is available as part of the BioJava-legacy
(v 1.8) project.

BioJava3 currently does not have a Genbank parser yet, only fasta. I
added it to the (new) missing features page :

http://www.biojava.org/wiki/BioJava3_Feature_Requests

Andreas



On Sun, Oct 30, 2011 at 7:54 PM, Ed Beaty <edbeaty at charter.net> wrote:
> Hello all. ?Is it possible to import Genbank (*.gb) format files using BioJava 3? ?I can't find the SeqIOTools class described in the GeneralReader example in the http://www.biojava.org/docs/bj_in_anger/ReadingGES.htm doc.
> Thanks,
> Ed Beaty
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



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From: member at linkedin.com (Huijie Qiao via LinkedIn)
Date: Wed, 2 Nov 2011 02:57:54 +0000 (UTC)
Subject: [Biojava-l] Invitation to connect on LinkedIn
Message-ID: <1927181069.419433.1320202674916.JavaMail.app@ela4-bed82.prod>

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From biojava at hannes.oib.com  Thu Nov  3 13:08:22 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 3 Nov 2011 14:08:22 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
Message-ID: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>

Hi!

Is there a Class/Method in Biojava that calculates the Levenshtein
distance between two sequences? I could not find anything in the docs
at first search.

I need to compare 2 DNASequences (or Strings) and get the number of
insertions, deletions, and substitutions. Ideally, there would be an
option to abort the comparison if the number of mismatches exceeds a
certain number.

Hannes


From biojava at hannes.oib.com  Thu Nov  3 14:17:05 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Thu, 3 Nov 2011 15:17:05 +0100
Subject: [Biojava-l] Sequence Alignment and IUB Codes
Message-ID: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>

Does the biojava sequence alignment support IUB Codes?
http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation

Hannes


From andreas at sdsc.edu  Fri Nov  4 06:18:12 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 3 Nov 2011 23:18:12 -0700
Subject: [Biojava-l] Sequence Alignment and IUB Codes
In-Reply-To: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
References: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
Message-ID: <CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>

Hi Hannes,

I think that depends which substitution matrix you are using. Some of
them don't support ambiguity codes.

Andreas

On Thu, Nov 3, 2011 at 7:17 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Does the biojava sequence alignment support IUB Codes?
> http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation
>
> Hannes
> _______________________________________________
> 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 Nov  4 06:20:53 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Fri, 4 Nov 2011 07:20:53 +0100
Subject: [Biojava-l] Sequence Alignment and IUB Codes
In-Reply-To: <CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>
References: <CAPXi2mnO+kGHCc+iw1Gce7zffjvYZf550eSpjJ7KmPHPbObxjA@mail.gmail.com>
	<CALthepxkwCrZfL0sKj7QWPGO_A6zVFS-R30oszEdJtuCt-XbTA@mail.gmail.com>
Message-ID: <CAPXi2mnR=4H3ZOHP=iPPPSZ16CAm+dnvxX6Ak1=30oF7V-i+kQ@mail.gmail.com>

Thanks Andreas, of course, that's where I can configure it. Thanks for
the clarification.
Hannes

On Fri, Nov 4, 2011 at 07:18, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes,
>
> I think that depends which substitution matrix you are using. Some of
> them don't support ambiguity codes.
>
> Andreas
>
> On Thu, Nov 3, 2011 at 7:17 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Does the biojava sequence alignment support IUB Codes?
>> http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation
>>
>> Hannes
>> _______________________________________________
>> 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 Nov  4 06:21:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Thu, 3 Nov 2011 23:21:57 -0700
Subject: [Biojava-l] BioJava in education
Message-ID: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>

Hi,

Is anybody using BioJava in teaching, or has been introduced to
BioJava as part of a course?

Andreas


From cfriedline at vcu.edu  Fri Nov  4 13:50:52 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Fri, 4 Nov 2011 09:50:52 -0400
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>

Andreas, 

I had to come to it on my own.  Seems the focus at this university is on Perl only and there's a serious (IMO) disconnect with our CS department.  Java (or some other OO language) is only a minor requirement for bioinformatics undergrads/graduate students.  However, I'd love to see this change and/or be involved in the development of a course to do just that.  We've been kicking around developing some intersession modules around dealing with genetic data sets using Java/BioJava, but doing actual research continues to stand in our way.

On a side note, have you seen the Java Evolutionary Biology Library?  Would be excellent to combine forces of these development efforts since JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely from a selfish user perspective.  ;-)

Chris

On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:

> Hi,
> 
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
> 
> Andreas
> _______________________________________________
> 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 Nov  4 23:11:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Nov 2011 16:11:46 -0700
Subject: [Biojava-l] BioJava in education
In-Reply-To: <B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
Message-ID: <CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>

Hi,

to quickly follow up: A few people have contacted me off list that
they were introduced to BioJava through some course. Interestingly no
teachers though who arranged this. I would be interested in organising
the exchange of teaching materials. If anybody wants to exchange power
points, homework assignment ideas, etc.  please let me know.


Chris wrote:
> On a side note, have you seen the Java Evolutionary Biology Library? ?Would be excellent to combine forces of these development efforts since JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely from a selfish user perspective. ?;-)

That is a great suggestion. Seems that project does not really have a
web presence. Any idea how to contact the main developers? There is no
mailing list. I guess one could try via sourceforge somehow.

Andreas




> Chris
>
> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>
>> Hi,
>>
>> Is anybody using BioJava in teaching, or has been introduced to
>> BioJava as part of a course?
>>
>> Andreas
>> _______________________________________________
>> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>



From simon.rayner.cn at gmail.com  Fri Nov  4 23:18:33 2011
From: simon.rayner.cn at gmail.com (simon rayner)
Date: Sat, 5 Nov 2011 07:18:33 +0800
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
Message-ID: <CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>

i've been trying to use biojava as a segment of an advanced bioinformatics
course for masters students but these are students who are studying
virology with a specific interest in bioinformatics.  Nevertheless, some
students take to it very easily but, for me, it seems the major drawback
with biojava is it is a lot more disjointed compared to bioperl,. By this i
mean, it's not always easy to find the classes you need, or if the class is
available, it was broken during a previous release, or simply wasn't
included in the latest version. I think biojava is the way to go for
training and a course development project might be the way to get a more
cohesive documentation set.

On Fri, Nov 4, 2011 at 9:50 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>
>> Andreas,
>>
>> I had to come to it on my own.  Seems the focus at this university is on
>> Perl only and there's a serious (IMO) disconnect with our CS department.
>>  Java (or some other OO language) is only a minor requirement for
>> bioinformatics undergrads/graduate students.  However, I'd love to see this
>> change and/or be involved in the development of a course to do just that.
>>  We've been kicking around developing some intersession modules around
>> dealing with genetic data sets using Java/BioJava, but doing actual
>> research continues to stand in our way.
>>
>> On a side note, have you seen the Java Evolutionary Biology Library?
>>  Would be excellent to combine forces of these development efforts since
>> JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely
>> from a selfish user perspective.  ;-)
>>
>> Chris
>>
>> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>>
>> > Hi,
>> >
>> > Is anybody using BioJava in teaching, or has been introduced to
>> > BioJava as part of a course?
>> >
>> > Andreas
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895 (office)
> +86 18627113001 (cell)
>
>


-- 
Simon Rayner

State Key Laboratory of Virology
Wuhan Institute of Virology
Chinese Academy of Sciences
Wuhan, Hubei 430071
P.R.China

+86 (27) 87199895 (office)
+86 18627113001 (cell)


From andreas at sdsc.edu  Sat Nov  5 00:37:03 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 4 Nov 2011 17:37:03 -0700
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CAHo9xw++3-fkYANDgb=1eTNbN5KA1ejmiksr6R72bzaA91eMDw@mail.gmail.com>
	<CAHo9xwKSPiJcbWoDPRnOCTpcWHESdx77rpA-09ZHVuVxE-eF4g@mail.gmail.com>
Message-ID: <CALthepwgcRJs+1dsyCLGhG-ovvwf1kLUdYpYcO_j5JVqxhbQMA@mail.gmail.com>

Thanks Simon, v. interesting. Can you provide some more details? What
kind of tasks were you requiring the students to perform? I agree, a
project to prepare course material would be great.

Andreas

On Fri, Nov 4, 2011 at 4:18 PM, simon rayner <simon.rayner.cn at gmail.com> wrote:
> i've been trying to use biojava as a segment of an advanced bioinformatics
> course for masters students but these are students who are studying
> virology with a specific interest in bioinformatics. ?Nevertheless, some
> students take to it very easily but, for me, it seems the major drawback
> with biojava is it is a lot more disjointed compared to bioperl,. By this i
> mean, it's not always easy to find the classes you need, or if the class is
> available, it was broken during a previous release, or simply wasn't
> included in the latest version. I think biojava is the way to go for
> training and a course development project might be the way to get a more
> cohesive documentation set.
>
> On Fri, Nov 4, 2011 at 9:50 PM, Chris Friedline <cfriedline at vcu.edu> wrote:
>>
>>> Andreas,
>>>
>>> I had to come to it on my own. ?Seems the focus at this university is on
>>> Perl only and there's a serious (IMO) disconnect with our CS department.
>>> ?Java (or some other OO language) is only a minor requirement for
>>> bioinformatics undergrads/graduate students. ?However, I'd love to see this
>>> change and/or be involved in the development of a course to do just that.
>>> ?We've been kicking around developing some intersession modules around
>>> dealing with genetic data sets using Java/BioJava, but doing actual
>>> research continues to stand in our way.
>>>
>>> On a side note, have you seen the Java Evolutionary Biology Library?
>>> ?Would be excellent to combine forces of these development efforts since
>>> JEBL is well-vetted (e.g., FigTree, BEAST, Geneious), though that's purely
>>> from a selfish user perspective. ?;-)
>>>
>>> Chris
>>>
>>> On Nov 4, 2011, at 2:21 AM, Andreas Prlic wrote:
>>>
>>> > Hi,
>>> >
>>> > Is anybody using BioJava in teaching, or has been introduced to
>>> > BioJava as part of a course?
>>> >
>>> > Andreas
>>> > _______________________________________________
>>> > 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
>>>
>>
>>
>>
>> --
>> Simon Rayner
>>
>> State Key Laboratory of Virology
>> Wuhan Institute of Virology
>> Chinese Academy of Sciences
>> Wuhan, Hubei 430071
>> P.R.China
>>
>> +86 (27) 87199895 (office)
>> +86 18627113001 (cell)
>>
>>
>
>
> --
> Simon Rayner
>
> State Key Laboratory of Virology
> Wuhan Institute of Virology
> Chinese Academy of Sciences
> Wuhan, Hubei 430071
> P.R.China
>
> +86 (27) 87199895?(office)
> +86 18627113001?(cell)
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From cfriedline at vcu.edu  Sat Nov  5 14:18:18 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Sat, 5 Nov 2011 10:18:18 -0400
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
	<B885501C-681B-41DD-A483-E76CF34C638F@vcu.edu>
	<CALthepwa7B+XAivzvPFGP9zNYcc+OCzk2n8myEZ9SYbkurvnBA@mail.gmail.com>
Message-ID: <9B411F3A-FCC2-449A-9F3C-44AD91DF30BD@vcu.edu>


On Nov 4, 2011, at 7:11 PM, Andreas Prlic wrote:

> 
> That is a great suggestion. Seems that project does not really have a
> web presence. Any idea how to contact the main developers? There is no
> mailing list. I guess one could try via sourceforge somehow.

You may want to contact either Alexei Drummond (http://compevol.auckland.ac.nz/people/)
or Andrew Rambaut (http://tree.bio.ed.ac.uk/).  I think their emails are on their respective sites.

Chris 


From biojava at hannes.oib.com  Mon Nov  7 13:39:16 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Mon, 7 Nov 2011 14:39:16 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
Message-ID: <CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>

Following up:

If there is no such thing, should I make it available if I write it?

Hannes

On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Hi!
>
> Is there a Class/Method in Biojava that calculates the Levenshtein
> distance between two sequences? I could not find anything in the docs
> at first search.
>
> I need to compare 2 DNASequences (or Strings) and get the number of
> insertions, deletions, and substitutions. Ideally, there would be an
> option to abort the comparison if the number of mismatches exceeds a
> certain number.
>
> Hannes
>



From andreas at sdsc.edu  Mon Nov  7 14:42:57 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Mon, 7 Nov 2011 06:42:57 -0800
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
Message-ID: <CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>

Hi Hannes,

you are right, this does not exist yet. Somebody else asked the same
question a few weeks ago. As such it would be great if you could
provide a patch, there might be other people interested in that, too.

Andreas

On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Following up:
>
> If there is no such thing, should I make it available if I write it?
>
> Hannes
>
> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Hi!
>>
>> Is there a Class/Method in Biojava that calculates the Levenshtein
>> distance between two sequences? I could not find anything in the docs
>> at first search.
>>
>> I need to compare 2 DNASequences (or Strings) and get the number of
>> insertions, deletions, and substitutions. Ideally, there would be an
>> option to abort the comparison if the number of mismatches exceeds a
>> certain number.
>>
>> Hannes
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From forumjspro at gmail.com  Mon Nov  7 15:03:55 2011
From: forumjspro at gmail.com (forumjspro at gmail.com)
Date: Mon, 7 Nov 2011 16:03:55 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
Message-ID: <6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>

Hi Hannes,

You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors. 

But it will not stop when a maximal number of errors is reached ...

JS

Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :

> Hi Hannes,
> 
> you are right, this does not exist yet. Somebody else asked the same
> question a few weeks ago. As such it would be great if you could
> provide a patch, there might be other people interested in that, too.
> 
> Andreas
> 
> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Following up:
>> 
>> If there is no such thing, should I make it available if I write it?
>> 
>> Hannes
>> 
>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Hi!
>>> 
>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>> distance between two sequences? I could not find anything in the docs
>>> at first search.
>>> 
>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>> insertions, deletions, and substitutions. Ideally, there would be an
>>> option to abort the comparison if the number of mismatches exceeds a
>>> certain number.
>>> 
>>> Hannes
>>> 
>> 
>> _______________________________________________
>> 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 cfriedline at vcu.edu  Mon Nov  7 15:58:28 2011
From: cfriedline at vcu.edu (Chris Friedline)
Date: Mon, 7 Nov 2011 10:58:28 -0500
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
Message-ID: <7E0C3BDA-03F4-4723-BE91-0F4B274DD671@vcu.edu>

Hannes,

If you really want to use Levenstein distance, there's a method in Apache commons lang StringUtils.

Chris

On Nov 3, 2011, at 9:08 AM, Hannes Brandst?tter-M?ller wrote:

> Hi!
> 
> Is there a Class/Method in Biojava that calculates the Levenshtein
> distance between two sequences? I could not find anything in the docs
> at first search.
> 
> I need to compare 2 DNASequences (or Strings) and get the number of
> insertions, deletions, and substitutions. Ideally, there would be an
> option to abort the comparison if the number of mismatches exceeds a
> certain number.
> 
> Hannes
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l




From amr_alhossary at hotmail.com  Mon Nov  7 14:48:28 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Mon, 7 Nov 2011 16:48:28 +0200
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <BLU150-ds1385430025799F5590E8428ED90@phx.gbl>

Sorry for the late reply.
Although I come into it on my own, I had the interest to voluntarily teach 
it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
I focused on BioJava 1.7 and I May send you the presentation if you like.
Unfortunately, this department was closed after 2 successive intakes, so I 
didn't update it.


Amr

--------------------------------------------------
From: "Andreas Prlic" <andreas at sdsc.edu>
Sent: Friday, November 04, 2011 8:21 AM
To: "Biojava" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] BioJava in education

> Hi,
>
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
>
> Andreas
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 


From amr_alhossary at hotmail.com  Mon Nov  7 14:48:28 2011
From: amr_alhossary at hotmail.com (Amr AL-Hossary)
Date: Mon, 7 Nov 2011 16:48:28 +0200
Subject: [Biojava-l] BioJava in education
In-Reply-To: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
References: <CALthepzkShLE8=uHxBcULwFNfen+bHmYMyGDx+g51KP2WaeZaA@mail.gmail.com>
Message-ID: <BLU150-ds10D8DB258F16931B2627268ED90@phx.gbl>

Sorry for the late reply.
Although I come into it on my own, I had the interest to voluntarily teach 
it to the Bioinforamtics group of ITi (a famous IT Institute herein Egypt).
I focused on BioJava 1.7 and I May send you the presentation if you like.
Unfortunately, this department was closed after 2 successive intakes, so I 
didn't update it.


Amr

--------------------------------------------------
From: "Andreas Prlic" <andreas at sdsc.edu>
Sent: Friday, November 04, 2011 8:21 AM
To: "Biojava" <biojava-l at lists.open-bio.org>
Subject: [Biojava-l] BioJava in education

> Hi,
>
> Is anybody using BioJava in teaching, or has been introduced to
> BioJava as part of a course?
>
> Andreas
> _______________________________________________
> 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  Wed Nov  9 09:01:15 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Wed, 9 Nov 2011 10:01:15 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
Message-ID: <CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>

Thanks.

I am thinking about implementing a modified MatrixAligner to fit my
needs here. Direct Levenstein Distance is not exactly right for my
application, because there are 0 to n insertions/deletions.

A direct LevensteinDistance as implemented in would not give me all
the Information I need.

Thanks for the hints and input.

Hannes

PS we seriously need more examples in the Cookbook - I'll submit some
later, but the modified N-W Aligner mentioned below would make a good
example too, don't you think? ;)

On Mon, Nov 7, 2011 at 16:03,  <forumjspro at gmail.com> wrote:
> Hi Hannes,
>
> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>
> But it will not stop when a maximal number of errors is reached ...
>
> JS
>
> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>
>> Hi Hannes,
>>
>> you are right, this does not exist yet. Somebody else asked the same
>> question a few weeks ago. As such it would be great if you could
>> provide a patch, there might be other people interested in that, too.
>>
>> Andreas
>>
>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>> <biojava at hannes.oib.com> wrote:
>>> Following up:
>>>
>>> If there is no such thing, should I make it available if I write it?
>>>
>>> Hannes
>>>
>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Hi!
>>>>
>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>> distance between two sequences? I could not find anything in the docs
>>>> at first search.
>>>>
>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>> option to abort the comparison if the number of mismatches exceeds a
>>>> certain number.
>>>>
>>>> Hannes
>>>>
>>>
>>> _______________________________________________
>>> 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 khalil.elmazouari at gmail.com  Mon Nov 14 16:00:37 2011
From: khalil.elmazouari at gmail.com (Khalil El Mazouari)
Date: Mon, 14 Nov 2011 17:00:37 +0100
Subject: [Biojava-l] Rename RichSequence
Message-ID: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>

Hi,

how to rename a RichSequence?

Thanks



From Dietmar.Birzer at biologie.uni-regensburg.de  Mon Nov 14 16:53:29 2011
From: Dietmar.Birzer at biologie.uni-regensburg.de (Dietmar Birzer)
Date: Mon, 14 Nov 2011 17:53:29 +0100
Subject: [Biojava-l] Exception thrown when parsing GenBank file
Message-ID: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>


Hi all, 

I am currently trying to debug a little software application which uses BioJava's core-1.8.1.jar library because it has started to throw exceptions a while ago.  

I guess the problem is, that the GenbankLocationParser is not able to handle "Het" entries in the features section of the GenBank/GenPept format, e.g.  

 Het             join(bond(9),bond(125))  
                     /heterogen="( NA,   5 )"  

for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .  

Calling   

new GenpeptRichSequenceDB().getRichSequence("14719485");  

will result in an error message like:  

Error while querying 14719485!  
org.biojava.bio.BioException: Failed to read Genbank sequence  
at org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:158)  
Caused by: org.biojava.bio.BioException: Could not read sequence  
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:113)  
at org.biojavax.bio.db.ncbi.GenpeptRichSequenceDB.getRichSequence(GenpeptRichSequenceDB.java:154)  
... 2 more  
Caused by: org.biojava.bio.seq.io.ParseException: Could not understand position: bond(9  
at org.biojavax.bio.seq.io.GenbankLocationParser.parsePosition(GenbankLocationParser.java:286)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:272)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocString(GenbankLocationParser.java:237)  
at org.biojavax.bio.seq.io.GenbankLocationParser.parseLocation(GenbankLocationParser.java:132)  
at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:508)  
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)  
... 3 more  

I have checked several other database entires and none of the ones that worked had a "Het" entry. But I also failed at 56965892, 13786715, 209156668 and 12084365. Has anybody else come across this problem or knows how to fix it?  

Thanks,  
 Dietmar



From p.j.a.cock at googlemail.com  Mon Nov 14 17:29:31 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 14 Nov 2011 17:29:31 +0000
Subject: [Biojava-l] Exception thrown when parsing GenBank file
In-Reply-To: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
Message-ID: <CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>

On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>
> Hi all,
>
> I am currently trying to debug a little software application which
> uses BioJava's core-1.8.1.jar library because it has started to
> throw exceptions a while ago.
>
> I guess the problem is, that the GenbankLocationParser is not
> able to handle "Het" entries in the features section of the
> GenBank/GenPept format, e.g.
>
> ?Het ? ? ? ? ? ? join(bond(9),bond(125))
> ? ? ? ? ? ? ? ? ? ? /heterogen="( NA, ? 5 )"
>
> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .

Interesting - note the bond locations are not in the official
DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
that seems to be intended only for nucleotides and not proteins as here.
It might be worth contacting the NCBI to find out if there is an official
specification covering these location strings?

Peter



From gwaldon at geneinfinity.org  Mon Nov 14 23:20:02 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Mon, 14 Nov 2011 17:20:02 -0600
Subject: [Biojava-l] Rename RichSequence
In-Reply-To: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>
References: <97C210D8-F5C4-4E0D-AF59-FDB4BCE193F7@gmail.com>
Message-ID: <20111114172002.19321y9clytb4ug0@gator1273.hostgator.com>

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

> Hi,
>
> how to rename a RichSequence?
>
> Thanks
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

Hi,

You cannot rename SimpleRichSequence by design. A simple way is to  
wrap the sequence in your own implementation of RichSequence and  
delegate to it.

Regards,
George



From biojava at hannes.oib.com  Tue Nov 15 14:10:43 2011
From: biojava at hannes.oib.com (=?ISO-8859-1?Q?Hannes_Brandst=E4tter=2DM=FCller?=)
Date: Tue, 15 Nov 2011 15:10:43 +0100
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
	<CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
Message-ID: <CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>

Well, I have implemented a first version that is running quite well
for me and my needs/specifications, although I did not integrate it
directly into the biojava class hierarchy yet.
Is anyone interested in taking a look at it and giving me some
feedback if I shoud invest the time and work to make it includable
into biojava?

Hannes

On Wed, Nov 9, 2011 at 10:01, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Thanks.
>
> I am thinking about implementing a modified MatrixAligner to fit my
> needs here. Direct Levenstein Distance is not exactly right for my
> application, because there are 0 to n insertions/deletions.
>
> A direct LevensteinDistance as implemented in would not give me all
> the Information I need.
>
> Thanks for the hints and input.
>
> Hannes
>
> PS we seriously need more examples in the Cookbook - I'll submit some
> later, but the modified N-W Aligner mentioned below would make a good
> example too, don't you think? ;)
>
> On Mon, Nov 7, 2011 at 16:03, ?<forumjspro at gmail.com> wrote:
>> Hi Hannes,
>>
>> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>>
>> But it will not stop when a maximal number of errors is reached ...
>>
>> JS
>>
>> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>>
>>> Hi Hannes,
>>>
>>> you are right, this does not exist yet. Somebody else asked the same
>>> question a few weeks ago. As such it would be great if you could
>>> provide a patch, there might be other people interested in that, too.
>>>
>>> Andreas
>>>
>>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>>> <biojava at hannes.oib.com> wrote:
>>>> Following up:
>>>>
>>>> If there is no such thing, should I make it available if I write it?
>>>>
>>>> Hannes
>>>>
>>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Hi!
>>>>>
>>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>>> distance between two sequences? I could not find anything in the docs
>>>>> at first search.
>>>>>
>>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>>> option to abort the comparison if the number of mismatches exceeds a
>>>>> certain number.
>>>>>
>>>>> Hannes
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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 andreas at sdsc.edu  Tue Nov 15 15:53:50 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 15 Nov 2011 07:53:50 -0800
Subject: [Biojava-l] Calculating edit distance between 2 DNA Sequences
In-Reply-To: <CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>
References: <CAPXi2mkr452JMDZkDuMS0+cDc+kZwRyV-h_raR=mkMLGhYuHbg@mail.gmail.com>
	<CAPXi2mkrnF3WUrOouCwm96HO32iVbNYLaMzU0vuPhB5v4O9vRw@mail.gmail.com>
	<CALthepyuTfmjLd9My0vGMUbMc39CE+QEUR84PO-stpDcKjYtHw@mail.gmail.com>
	<6671E3C3-790E-4545-B228-17D8238DD81C@gmail.com>
	<CAPXi2m=34ook1C=jtw1b1x8E2-iHYbN-e9VCN1jNN46Eoy8_ig@mail.gmail.com>
	<CAPXi2m=rh+6RqyS9yMdiGNNGcqrVt7QT=WbSV_dbZAkVB=bVoQ@mail.gmail.com>
Message-ID: <CALthepz=w8z73=yGSqX+GM-q-nwJSdRd+kokE8EHZUL3GgJWpw@mail.gmail.com>

you could send it to the list here and ask for feedback..

Andreas

On Tue, Nov 15, 2011 at 6:10 AM, Hannes Brandst?tter-M?ller
<biojava at hannes.oib.com> wrote:
> Well, I have implemented a first version that is running quite well
> for me and my needs/specifications, although I did not integrate it
> directly into the biojava class hierarchy yet.
> Is anyone interested in taking a look at it and giving me some
> feedback if I shoud invest the time and work to make it includable
> into biojava?
>
> Hannes
>
> On Wed, Nov 9, 2011 at 10:01, Hannes Brandst?tter-M?ller
> <biojava at hannes.oib.com> wrote:
>> Thanks.
>>
>> I am thinking about implementing a modified MatrixAligner to fit my
>> needs here. Direct Levenstein Distance is not exactly right for my
>> application, because there are 0 to n insertions/deletions.
>>
>> A direct LevensteinDistance as implemented in would not give me all
>> the Information I need.
>>
>> Thanks for the hints and input.
>>
>> Hannes
>>
>> PS we seriously need more examples in the Cookbook - I'll submit some
>> later, but the modified N-W Aligner mentioned below would make a good
>> example too, don't you think? ;)
>>
>> On Mon, Nov 7, 2011 at 16:03, ?<forumjspro at gmail.com> wrote:
>>> Hi Hannes,
>>>
>>> You could do such a comparison by using the Needleman-Wunsh aligner with gap penalty set to -1 and the matrix set to -1 for mismatches and 0 for matches. The absolute value of the resulting score is exactly the number of errors.
>>>
>>> But it will not stop when a maximal number of errors is reached ...
>>>
>>> JS
>>>
>>> Le 7 nov. 2011 ? 15:42, Andreas Prlic a ?crit :
>>>
>>>> Hi Hannes,
>>>>
>>>> you are right, this does not exist yet. Somebody else asked the same
>>>> question a few weeks ago. As such it would be great if you could
>>>> provide a patch, there might be other people interested in that, too.
>>>>
>>>> Andreas
>>>>
>>>> On Mon, Nov 7, 2011 at 5:39 AM, Hannes Brandst?tter-M?ller
>>>> <biojava at hannes.oib.com> wrote:
>>>>> Following up:
>>>>>
>>>>> If there is no such thing, should I make it available if I write it?
>>>>>
>>>>> Hannes
>>>>>
>>>>> On Thu, Nov 3, 2011 at 14:08, Hannes Brandst?tter-M?ller
>>>>> <biojava at hannes.oib.com> wrote:
>>>>>> Hi!
>>>>>>
>>>>>> Is there a Class/Method in Biojava that calculates the Levenshtein
>>>>>> distance between two sequences? I could not find anything in the docs
>>>>>> at first search.
>>>>>>
>>>>>> I need to compare 2 DNASequences (or Strings) and get the number of
>>>>>> insertions, deletions, and substitutions. Ideally, there would be an
>>>>>> option to abort the comparison if the number of mismatches exceeds a
>>>>>> certain number.
>>>>>>
>>>>>> Hannes
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>>
>>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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



From lfrohman at gmail.com  Wed Nov 16 16:14:18 2011
From: lfrohman at gmail.com (Lance Frohman)
Date: Wed, 16 Nov 2011 08:14:18 -0800
Subject: [Biojava-l] biojava-ensembl
Message-ID: <CAOseA7ww6OoX50Ha2UwqP-6cJ_-PLb9vGaCkghrV0eqb_H2hag@mail.gmail.com>

Where do I find the source code for biojava-ensembl?

thanks


From Dietmar.Birzer at biologie.uni-regensburg.de  Wed Nov 23 15:18:29 2011
From: Dietmar.Birzer at biologie.uni-regensburg.de (Dietmar Birzer)
Date: Wed, 23 Nov 2011 16:18:29 +0100
Subject: [Biojava-l] Antw: Re:  Exception thrown when parsing GenBank file
In-Reply-To: <CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
Message-ID: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>

 Hi all,

as the GenbankLocationParser from biojava-1.8.1 is not working properly anymore, I was wondering if there is an equivalent way to do this ( GenpeptRichSequenceDB().getRichSequence("14719485") ) using BioJava 3.
Unfortunately I could not find any GenBank/GenPept parser so far. Is that because it does not exist (yet), or just because I have not looked properly?

Best wishes
 Dietmar
 
>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>> 
On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>
> Hi all,
>
> I am currently trying to debug a little software application which
> uses BioJava's core-1.8.1.jar library because it has started to
> throw exceptions a while ago.
>
> I guess the problem is, that the GenbankLocationParser is not
> able to handle "Het" entries in the features section of the
> GenBank/GenPept format, e.g.
>
>  Het             join(bond(9),bond(125))
>                     /heterogen="( NA,   5 )"
>
> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .

Interesting - note the bond locations are not in the official
DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
that seems to be intended only for nucleotides and not proteins as here.
It might be worth contacting the NCBI to find out if there is an official
specification covering these location strings?

Peter





From andreas at sdsc.edu  Wed Nov 23 15:34:46 2011
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 23 Nov 2011 07:34:46 -0800
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
Message-ID: <CALthepxMGfTsFH8UyHJ2==wUqbXpBJXmLNjrY2HTqOsga_Ro=w@mail.gmail.com>

Hi Dietmar,

The genbank parser is on top of the feature request list for biojava
3: http://biojava.org/wiki/BioJava3_Feature_Requests

Anybody who wants to take an initiative here and claim ownership of
this topic is welcome...

Andreas


On Wed, Nov 23, 2011 at 7:18 AM, Dietmar Birzer
<Dietmar.Birzer at biologie.uni-regensburg.de> wrote:
> ?Hi all,
>
> as the GenbankLocationParser from biojava-1.8.1 is not working properly anymore, I was wondering if there is an equivalent way to do this ( GenpeptRichSequenceDB().getRichSequence("14719485") ) using BioJava 3.
> Unfortunately I could not find any GenBank/GenPept parser so far. Is that because it does not exist (yet), or just because I have not looked properly?
>
> Best wishes
> ?Dietmar
>
>>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>>
> On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>>
>> Hi all,
>>
>> I am currently trying to debug a little software application which
>> uses BioJava's core-1.8.1.jar library because it has started to
>> throw exceptions a while ago.
>>
>> I guess the problem is, that the GenbankLocationParser is not
>> able to handle "Het" entries in the features section of the
>> GenBank/GenPept format, e.g.
>>
>> ?Het ? ? ? ? ? ? join(bond(9),bond(125))
>> ? ? ? ? ? ? ? ? ? ? /heterogen="( NA, ? 5 )"
>>
>> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
>
> Interesting - note the bond locations are not in the official
> DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
>
> However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
> that seems to be intended only for nucleotides and not proteins as here.
> It might be worth contacting the NCBI to find out if there is an official
> specification covering these location strings?
>
> Peter
>
>
>
> _______________________________________________
> Biojava-l mailing list ?- ?Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



From gwaldon at geneinfinity.org  Wed Nov 23 16:06:57 2011
From: gwaldon at geneinfinity.org (George Waldon)
Date: Wed, 23 Nov 2011 10:06:57 -0600
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
Message-ID: <20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>

Hi Dietmar,

The GenbankLocationParser from biojava-1.8.1 is working perfectly as  
long as you feed him with DNA locations that use the syntax described  
in the DDBJ/EMBL/GenBank feature table definition. What you've got  
(join(bond(9),bond(125))...) is a pseudo GenBank format that  
apparently describes protein structure and uses a slightly different  
syntax to indicate heteroatom locations. That is why you get all these  
exceptions thrown.

George



Quoting Dietmar Birzer <Dietmar.Birzer at biologie.uni-regensburg.de>:

>  Hi all,
>
> as the GenbankLocationParser from biojava-1.8.1 is not working  
> properly anymore, I was wondering if there is an equivalent way to  
> do this ( GenpeptRichSequenceDB().getRichSequence("14719485") )  
> using BioJava 3.
> Unfortunately I could not find any GenBank/GenPept parser so far. Is  
> that because it does not exist (yet), or just because I have not  
> looked properly?
>
> Best wishes
>  Dietmar
>
>>>> Peter Cock <p.j.a.cock at googlemail.com> 11/14/2011 6:29 PM >>>
> On Mon, Nov 14, 2011 at 4:53 PM, Dietmar Birzer wrote:
>>
>> Hi all,
>>
>> I am currently trying to debug a little software application which
>> uses BioJava's core-1.8.1.jar library because it has started to
>> throw exceptions a while ago.
>>
>> I guess the problem is, that the GenbankLocationParser is not
>> able to handle "Het" entries in the features section of the
>> GenBank/GenPept format, e.g.
>>
>>  Het             join(bond(9),bond(125))
>>                     /heterogen="( NA,   5 )"
>>
>> for database id 14719485 (http://www.ncbi.nlm.nih.gov/protein/14719485) .
>
> Interesting - note the bond locations are not in the official
> DDBJ/EMBL/GenBank feature table specification (v9, Oct 2011):
> http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
>
> However, as noted on http://www.bioperl.org/wiki/BioPerl_Locations
> that seems to be intended only for nucleotides and not proteins as here.
> It might be worth contacting the NCBI to find out if there is an official
> specification covering these location strings?
>
> Peter
>
>
>
> _______________________________________________
> 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 Nov 23 17:01:11 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 23 Nov 2011 17:01:11 +0000
Subject: [Biojava-l] Antw: Re: Exception thrown when parsing GenBank file
In-Reply-To: <20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>
References: <4EC15599020000AA0001B58D@gwsmtp1.uni-regensburg.de>
	<CAKVJ-_4UXKoZ+QWZq0UDMthTfxw68XXJYhHgn+H=5p73wzsGUg@mail.gmail.com>
	<4ECD1CD5020000AA0001BADF@gwsmtp1.uni-regensburg.de>
	<20111123100657.23712tvrvitfya0w@gator1273.hostgator.com>
Message-ID: <CAKVJ-_49aO3P=GE6i+ULu_fSEw3LoA8v+1M3O5d9kG0wTxF0ag@mail.gmail.com>

On Wed, Nov 23, 2011 at 4:06 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Hi Dietmar,
>
> The GenbankLocationParser from biojava-1.8.1 is working perfectly as long as
> you feed him with DNA locations that use the syntax described in the
> DDBJ/EMBL/GenBank feature table definition.

As mentioned earlier, that document only covers nucleotide sequences,
not proteins as used in GenPept and the EMBL patents database:
http://lists.open-bio.org/pipermail/biojava-l/2011-November/007889.html

> What you've got (join(bond(9),bond(125))...) is a pseudo GenBank format
> that apparently describes protein structure and uses a slightly different
> syntax to indicate heteroatom locations. That is why you get all these
> exceptions thrown.
>
> George

It would be interesting to see if the EBI offer the same record(s) in
EMBL format, and if that too uses the (undocumented?) bond locations.

Peter