[Bioperl-l] new modules for sarching for patterns in fasta-files

Aaron J. Mackey amackey at pcbi.upenn.edu
Tue Aug 9 09:13:14 EDT 2005

Out of curiosity, are your patterns allowed to cross newlines  
embedded in the FASTA file?  This is the typical problem with using  
grep/agrep directly with sequence files ...


On Aug 8, 2005, at 1:12 PM, <markus.riester at student.uni-tuebingen.de>  
<markus.riester at student.uni-tuebingen.de> wrote:

> Hi,
> I've made some modules for searching for patterns in fasta files with
> different (really fast) backends like agrep and vmatch.  I don't  
> think you
> want to include this in standard bioperl. But we think it is useful  
> code and
> we'd like to share it on cpan. The main reason for this email is a  
> discussion
> about the right namespace for this module. What do you think?
> Markus
> (hope the attachment reaches the mailinglist, if not, please send  
> me a mail if
> you are interested in this code)
> <Weigel-Search-0.03.tar.gz>
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Aaron J. Mackey, Ph.D.
Project Manager, ApiDB Bioinformatics Resource Center
Penn Genomics Institute, University of Pennsylvania
email:  amackey at pcbi.upenn.edu
office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI)
fax:    215-746-6697
postal: Penn Genomics Institute
         Goddard Labs 212
         415 S. University Avenue
         Philadelphia, PA  19104-6017

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