[Bioperl-l] Genbank Bioperl help

[Brian Osborne]

Ali and Stefan,

Accession numbers starting with NP_ are Genbank RefSeq entries (see
http://www.ncbi.nlm.nih.gov/LocusLink/RSfaq.html). From the Bioperl FAQ:

  Q2.3: How can I get NT_ or NM_ accessions from NCBI (Reference
	Sequences)?

	Use Bio::DB::RefSeq not Bio::DB::GenBank when you are retrieving
	the NM_ accessions. This is still an area of active development
	because the data providers have not provided the best interface for
	us to query.  EBI has provided a mirror with their dbfetch system
	which is accessible through the Bio::DB::RefSeq object however,
	there are cases where NT_ accessions will not be retrievable.

Bio::DB::GenPept won't work, and a one-liner using Bio::DB::RefSeq seemed to
work. I'll change the FAQ so that it refers to NP_'s as well.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Stefan A Kirov
Sent: Wednesday, June 12, 2002 2:59 PM
To: Ali Al-Shahib
Cc: Bioperl
Subject: Re: [Bioperl-l] Genbank Bioperl help

Use Bio::DB::GenPept for proteins!
Good luck!
Stefan

On Wed, 12 Jun 2002, Ali Al-Shahib wrote:

>
>Hi
>
>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
>
>Ali
>--
>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
>
>
>
>
>
>
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