[Bioperl-l] bioperl genbank output is different than web?

Barry Moore bmoore at genetics.utah.edu
Sun Oct 16 07:21:50 EDT 2005


This is a known bug in bioperl 1.5 that has been fixed in the latest
release.  Get the new release (bioperl-1.5.1-rc3.tar.gz) here: 
http://bioperl.org/DIST and upgrade.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sam
Sent: Saturday, October 15, 2005 8:54 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] bioperl genbank output is different than web?


I am new to this so please forgive me for any dump

The problem: I am getting the genbank data for a gene
using the simple code below and writing it to a file.
The problem is that output is not the same as when I
do a web search via ncbi entrez.  I want to parse out
on which chromosome gene is on.  The web output gives
me a correct chromosome number (i.e. chromosome="3")
while the output from this code gives me (i.e.

Can someone help me figure out what is wrong please?

The Code:
use Bio::DB::GenBank;
use Bio::SeqIO;
use Bio::Seq;

$db_obj = Bio::DB::GenBank->new;
$seq_obj = $db_obj->get_Seq_by_acc("NM_011674");
$seqio_obj = Bio::SeqIO->new(-file
=>">data/genes/NM_011674.fa", -format=>"fasta");
$seqio_obj = Bio::SeqIO->new(-file
=>">data/genes/NM_011674.gb", -format=>"genbank");

Sam Al-Droubi, M.S.
saldroubi at yahoo.com
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