[Bioperl-l] Genbank Bioperl help

Ali Al-Shahib alshahib@dcs.gla.ac.uk
Wed, 12 Jun 2002 19:13:11 +0100 (BST)


I've got a set of accession numbers but they start with 'NP_' as they are 
proteins.  I've used the genbank module (Bio::DB::GenBank) and produced 
the following script:

#!/usr/local/bin/perl -w

use Bio::DB::GenBank;
use Bio::Species;
my $gb = new Bio::DB::GenBank;

#get a particular accession number
my $seq = $gb->get_Seq_by_acc('NP_347647');

#get the sepecies from the 'sequence' object
my $sp = $seq->species();

#get the classification
my @class = $sp->classification();

#print out the result, line by line
print join ("\n", @class), "\n";

However it works for accssion numbers for nucleotide sequences but not of 
protien sequences.  How can I change the script to make it fetch the 
organsim name from genbank using the protein accession number which starts 
with 'NP_' (example: NP_347647.1).  It fetches accession numbers like 
AC021953, but not 'NP_.....'.

I would greatly appreciate it if you can answer my query.

Thank you in advance

Mr Ali Al-Shahib
Research Student
Bioinformatics Research Centre
Department of Computing Science
17 Lilybank Gardens
University of Glasgow
Glasgow G12 8QQ
Scotland, UK
Tel: 0141 330 2421 (direct) 
E-mail: alshahib@dcs.gla.ac.uk
Web page: http://www.dcs.gla.ac.uk/~alshahib