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

hz5 at njit.edu hz5 at njit.edu
Fri Jan 6 00:30:43 EST 2006

NM is mRNA, should be separated by intron on genomic sequences, did you 
consider this when you search?

Quoting Sam Al-Droubi <saldroubi at yahoo.com>:

> All,
> 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
> ncbi 
> 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
> chromosome. 
> Thank you in advance. 
> Sincerely, 
> Sam Al-Droubi, M.S.
> saldroubi at yahoo.com
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Haibo Zhang, PhD
Computational Biology
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