[Bioperl-l] Can't find gene sequence in choromosome sequence

Barry Moore bmoore at genetics.utah.edu
Mon Oct 17 00:20:10 EDT 2005


Go to UCSC Genome database (http://genome.ucsc.edu).  Click on Table
Browser, Fill in the fields.  Your accession number goes under region:
position, and you want to select sequence as the output.  Click on get
output, choose genomic and then you'll get the option to specify how
much upstream sequence you'd like to include.


-----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: Sunday, October 16, 2005 7:43 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Can't find gene sequence in choromosome sequence


I downloaded the fasta sequence for a mouse gene from
genbank with accession number NM_01167.  I also
downloaded the Mouse chromosome 3 fasta file from from
The problem is that I can not find the gene sequence
in chromosome sequence. I used Perl
index($chr_obj->seq,$seq_obj->seq) and I get -1,
meaning no match.  I then searched by hand using grep
and emacs and to my surprise, the gene sequence is not
in the mm_chr3.fa file. What am I doing wrong?  Do I
have the wrong chromosome file?  I am positive that
this gene is in this chromosome according to genbank. 
By the way, I am doing this so that I can extract the
promoter region right before the gene starts on the

Thank you in advance. 


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