[Bioperl-l] Bio::DB::GenBank new(?) warning

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Aug 28 21:20:56 EDT 2012


What sequence identifiers are you using and what exactly are you trying to get?
Data is available via URL so a simple Perl script will retrieve that:
Eg.
http://eggnog.embl.de/version_3.0/cgi/groupview.py/?group=NOG285349&format=unaligned
http://eggnog.embl.de/version_3.0/cgi/groupview.py/?group=NOG285349&format=newick

I haven't tried it but will Bio::DB::EMBL work?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of maha ahmed
Sent: Wednesday, 29 August 2012 12:49 p.m.
To: Fields, Christopher J
Cc: Jim Hu; <bioperl-l at bioperl.org>
Subject: Re: [Bioperl-l] Bio::DB::GenBank new(?) warning

Hi guys,
I was searching for a bioperl script I can use to retrieve fasta sequences from the Eggnog database I only found ones to get sequences from Genbank, swissprot or ensembl Did anyone pass by any such script or knows a bioperl module that can be used to retrieve sequences from an online database If not then does anyone know a unix command that can be used to retrieve a sequence from an online database like eggnog

On Tue, Aug 28, 2012 at 10:02 PM, Fields, Christopher J < cjfields at illinois.edu> wrote:

> Is the BioProject DBSOURCE retained if you write the output back using 
> Bio::SeqIO?
>
> chris
>
> On Aug 28, 2012, at 1:09 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
> > I noticed that NCBI recently changed the path to genomes in their 
> > web
> interface. I'm wondering if that's related to my getting this kind of 
> message when I use Bio::DB::GenBank->get_Seq_by_acc()
> >
> > --------------------- WARNING ---------------------
> > MSG: Unrecognized DBSOURCE data: BioProject: PRJNA161931
> >
> > ---------------------------------------------------
> >
> > It still seems to work, though.
> >
> > Jim
> > =====================================
> > Jim Hu
> > Professor
> > Dept. of Biochemistry and Biophysics
> > 2128 TAMU
> > Texas A&M Univ.
> > College Station, TX 77843-2128
> > 979-862-4054
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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



More information about the Bioperl-l mailing list