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

Sam Al-Droubi saldroubi at yahoo.com
Sun Oct 16 09:42:37 EDT 2005


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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