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

Andrew Walsh walsh at cenix-bioscience.com
Fri Jan 6 03:35:57 EST 2006

If you look at the entry in the .gbs file (release 34.1), the exon 
coordinates for that mRNA are on the negative strand.  Are you using the 
transcript sequence or the gene sequence?  If you are using the gene 
sequence, reverse complementing should do the trick.  If you are using 
the transcript sequence, this will not work since you are missing the 


hz5 at njit.edu wrote:
> 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>:
>>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
> (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
>>Thank you in advance. 
>>Sam Al-Droubi, M.S.
>>saldroubi at yahoo.com
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
> =========================================================
> Haibo Zhang, PhD
> Computational Biology
> http://www.cyberpostdoc.org/
> Share postdoc information in cyberspace. Welcome your stories, suggestions and 
> advice!
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Andrew Walsh, M.Sc.
Senior Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Tatzberg 47
01307 Dresden
Tel. +49-351-4173 137
Fax  +49-351-4173 109

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