[Bioperl-l] get regions

Siddhartha Basu basu at pharm.sunysb.edu
Mon May 14 19:10:33 UTC 2007

Thiago Venancio wrote:
> Hi all,
> Using Bio::Seq, is there any easy way to get the coordinates where a
> regular expression matches or should I build a sliding window?
The perl core function "pos" should help you in this case. Do a 'perldoc
-f pos' for details.


> For example, looking for a given promoter region in a FASTA file. If
> the region is found, I would like to recover exactly the coordinates
> where it matches.
> Thanks in advance.
> Thiago

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