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Chris Fields | 1 Oct 2009 18:40
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FIrst alphas of BioPerl-Run, BioPerl-DB, BioPerl-Network

Just a quick note that the first alphas for BioPerl-Run, BioPerl-DB,  
and BioPerl-Network have been uploaded to CPAN:

http://search.cpan.org/~cjfields/BioPerl-Run-1.6.1_001/
http://search.cpan.org/~cjfields/BioPerl-DB-1.6.0_001/
http://search.cpan.org/~cjfields/BioPerl-Network-1.6.0_001/

And is available from the main BioPerl website:

http://bioperl.org/DIST/RC/BioPerl-Run-1.6.1_001.tar.gz
http://bioperl.org/DIST/RC/BioPerl-DB-1.6.0_001.tar.gz
http://bioperl.org/DIST/RC/BioPerl-Network-1.6.0_001.tar.gz

This is the first run where we've switched to a regular Module::Build  
installation, so expect some initial bumps!  There are a few initial  
problems that I plan on addressing soon, the main one being none of  
the modules are assigned version numbers (this may be a consequence of  
not pulling the version from a specific module).  The other, more  
serious one, is that the Build.PL script checks for DBI but isn't  
checking for any compatible DBD::* adaptors for BioPerl-DB (so it  
fails tests if DBI is installed).  We have code in core to check for  
DBI drivers, so I may adapt that for BioPerl-DB.

chris
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Emanuele Osimo | 1 Oct 2009 18:42
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computing gc content of a list of sequences

Dear all,
I have a multifasta file with a list of sequences.
How can I compute the gc % content of each of them? Is there a Bioperl tool?
Thanks
Emanuele
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Smithies, Russell | 1 Oct 2009 23:05
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Re: computing gc content of a list of sequences

Try bp_gccalc.pl

[smithiesr <at> impala ~]$ bp_gccalc.pl temp/sequences.fasta
Seq: 1  Len:149
GC content is 0.8255
Number of bases of type A= 22
Number of bases of type C= 49
Number of bases of type G= 74
Number of bases of type T= 4
--
Seq: 2  Len:5022
GC content is 0.5014
Number of bases of type A= 1282
Number of bases of type C= 1212
Number of bases of type G= 1306
Number of bases of type T= 1222
--
Seq: 3  Len:4923
GC content is 0.5452
Number of bases of type A= 1143
Number of bases of type C= 1307
Number of bases of type G= 1377
Number of bases of type T= 1096

--Russell

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
> bounces <at> lists.open-bio.org] On Behalf Of Emanuele Osimo
> Sent: Friday, 2 October 2009 5:42 a.m.
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Armin Schmitt | 2 Oct 2009 11:47
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Mutation analysis without liveseq objects

I would like to study the effect of DNA mutations.
Of special interest would be to find out if
a mutation causes an amino acid exchange or not.

Bio::LiveSeq::Mutator does a perfect
job, but the problem is that for many genes
no LiveSeq objects can be generated.

Does anybody know of a way how to perform
such an analysis with normal sequence objects?

Thank you very much.

Armin Schmitt

--

-- 
Dr. Armin Schmitt
Humboldt-Universität zu Berlin
Department for Crop and Animal Sciences
Invalidenstraße 42
10115 Berlin
Tel.:   +49-30-2093-9074
Fax:    +49-30-2093-6397
E-mail: armin.schmitt <at> agrar.hu-berlin.de
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Ben Busby | 2 Oct 2009 18:29
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Easily parsable command line BLAST output

Pardon the simple question, as I am new-ish to Perl, Bioperl, and
Computational Biology..
I am doing a whole bunch of large BLAST searches and am wondering what the
best command line BLAST commands are to put the output in a format best
parsable by Bio::SearchIO.

Thanks!

Ben

--

-- 
Economically, nothing is ever "extended by popular demand".
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Jason Stajich | 2 Oct 2009 18:41
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Re: Easily parsable command line BLAST output

Depends on what information you want to parse out.... do you need the  
actual alignment?  If no -> use -m 8 or -m 9 and you will have a  
tabular output that is easy to parse even without bioperl.

On Oct 2, 2009, at 9:29 AM, Ben Busby wrote:

> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering  
> what the
> best command line BLAST commands are to put the output in a format  
> best
> parsable by Bio::SearchIO.
>
> Thanks!
>
> Ben
>
>
>
> -- 
> Economically, nothing is ever "extended by popular demand".
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich <at> gmail.com
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Chris Fields | 2 Oct 2009 18:43
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Re: Easily parsable command line BLAST output

Ben,

The following has that information:

http://www.bioperl.org/wiki/Module:Bio::SearchIO
http://www.bioperl.org/wiki/HOWTO:SearchIO#Design

In short:

-m      type       SearchIO -format
0       text       blast
7       XML        blastxml
8       tabular    blasttable
9       tabular    blasttable

You should read the HOWTO and specific documentation for the  
Bio::SearchIO module just in case, and let us know if there are any  
spots that need improvement.

There are varied reports some of the alignment-based output is  
parsable via AlignIO somehow, but I haven't attempted it.

chris

On Oct 2, 2009, at 11:29 AM, Ben Busby wrote:

> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering  
> what the
(Continue reading)

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shalabh sharma | 2 Oct 2009 20:32
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Refseq/COG to EC

Hi All,           Is there any way i can convert or link Refseq id/COG to EC
number?
Is there any database or flat file which i can use for this purpose?

I would really appreciate if anyone can help me out.

Thanks
Shalabh
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Chris Fields | 5 Oct 2009 20:23
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Fwd: [Wg-phyloinformatics] NeXML schema update - RDFa-compliant metadata

Forwarding to bioperl-l just in case this wasn't noticed...

chris

Begin forwarded message:

> From: Jim Balhoff <balhoff <at> nescent.org>
> Date: October 5, 2009 1:11:50 PM CDT
> To: nexml-discuss <at> lists.sourceforge.net, DB Interop Hackathon <dbhack1 <at> nescent.org 
> >, Wg-phyloinformatics <at> nescent.org
> Subject: [Wg-phyloinformatics] NeXML schema update - RDFa-compliant  
> metadata
>
> Hi all (sorry for cross-posting),
>
> I have updated the NeXML schema to match the metadata requirements we
> came up with at the NESCent database interoperability hackathon last
> spring.  The changes have been committed to an SVN branch which can be
> browsed here:
>
> http://nexml.svn.sourceforge.net/viewvc/nexml/branches/rdfa-metadata/
>
> NeXML changes
> * All "id" attributes are now of type xs:ID instead of xs:NCName, and
> must be unique within a document.
> * All attributes used by one element to reference another (such as a
> "char" referring to its "states") are now of type xs:IDREF or
> xs:IDREFS (if multiple), and must refer to some valid ID in the
> document.
> * Removed <xs:attributeGroup ref="xml:specialAttrs" />  from the Base
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Denzel Li | 5 Oct 2009 20:35
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handling nexus files

Hello all:
Does bioperl support functions for handling nexus files? More specifically,
I need two functions, 1) combine multiple nexus files into one, 2) split a
nexus files into multiple nexus files. For example,
given the following two files  (file1.nex, file2.nex), is there function to
combine them into one file as shown in "combinedFile.nex", or to split
"combinedFile.nex" into two files (file1.nex, file2.nex).

------------------------------
# file1.nex
begin data;
  dimensions ntax=2 nchar=3
b1 GGG
b2 GGT
;end;
---------------------------------
# file2.nex
begin data;
  dimensions ntax=2 nchar=3
b1 AAA
b2 AAT
;end;
-------------------------------

# combinedFile.nex
begin data;
  dimensions ntax=2 nchar=6
[alignment from file1.nex]
b1 GGG
b2 GGT
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Gmane