[Bioperl-l] short motif searches

Sendu Bala bix at sendu.me.uk
Mon Oct 23 07:55:40 UTC 2006

Jyoti Shah wrote:
> Hi,
> I am interested in searching motifs as small as 6 or 7 nucleotides in
> genomic databases. I need exact matches. Is there any bioperl module
> available which can help me do this?

At 6 or 7bp long doing a simple exact match I should point out you're 
going to get very many hits; are you sure this is an appropriate thing 
to do for your purposes?

Assuming yes, you can use Bio::SeqIO, Bio::Index or Bio::DB::<something> 
to get your genomic sequences of interest, then simply use a normal perl 
regexp on the resulting $seq->seq strings.

If your motifs are anything like transcription factor binding sites, and 
you have more information than just a single sequence string for the 
motif, investigate Bio::Matrix::PSM.

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