[Bioperl-l] Get nucleotide sequence when expecting protein fromgenpept

[Chris Fields]

It's an imprted PIR record, so there probably is no accession recorded in
the database.  I think NCBI uses a fallback to nucleotide if it can't find a
particular accession via protein.  Using the primary ID (the GI#, 7498730)
works.  

Chris 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Frederick Partridge
> Sent: Tuesday, July 11, 2006 4:23 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Get nucleotide sequence when expecting protein
> fromgenpept
> 
> 
> 
> I am trying to retrieve various protein sequences from genpept using
> get_Seq_by_acc. All of them work ok, except one T16005:
> 
> 
> If I try and retrieve it with a reduced program:
> 
> 
> #!usr/bin/perl -w
> 
> use strict;
> 
> use Bio::Perl;
> use Bio::SeqIO;
> 
> my $genpept = new Bio::DB::GenPept;
> 
> my $seq = $genpept->get_Seq_by_acc('T16005');
> 
> print ($seq->seq(),'\n');
> 
> 
> 
> I get back a nucleotide sequence, which is another sequence at NCBI with
> the same accession number. (I thought these were meant to be unique? but
> evidently not.)
> 
> 
> I am using bioperl 1.5.1, perl 5.8.1, Mac OS 10.3
> 
> 
> Could anyone help me to get this protein sequence with my program?
> 
> 
> Many thanks,
> 
> 
> 
> Freddie Partridge
> 
> University of Oxford
> 
> 
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