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

Sam Al-Droubi saldroubi at yahoo.com
Sat Oct 15 22:54:22 EDT 2005


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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