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

[Sam Al-Droubi]

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 
(ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/Assembled_chromosomes/mm_chr3.fa.gz).
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