[Bioperl-l] amino acid sequence from a microbial gene id

Brian Osborne brian_osborne at cognia.com
Mon Jun 7 12:54:50 EDT 2004


That gene is a "feature" of the genomic sequence of S.c. For information on
how to get data from Genbank's feature table please see the
Feature-Annotation HOWTO, that's one approach. Another approach would be

molecular/scripts/db/schema>perl -e 'use Bio::DB::Query::GenBank; $query =
Bio::DB::Query::GenBank->new(-db => "protein", -query => "SCO5708"); $stream
= $gb->get_Stream_by_query($query);

Once you have $stream you could use it like this, of course:

while (my $seq = $stream->next_seq) {
	print $seq->seq,"\n";

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of jwon at ucalgary.ca
Sent: Monday, June 07, 2004 12:04 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] amino acid sequence from a microbial gene id


I have a gene I.D. from Streptomyces coelicolor (ie. SCO5708) and i wish to
retrieve the amino acid sequence that corresponds to it.  However, I can not
seem to find a method in Bio::DB::GenPept that will allow me to retrieve the
amino acid sequence by the gene I.D..  can anyone help me out with this?

thanks, jack
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org

More information about the Bioperl-l mailing list