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

maha ahmed mahakadry at aucegypt.edu
Tue Aug 28 20:48:58 EDT 2012


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
> >
> >
> >
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>
>
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