[Bioperl-l] Hmmsearch parsing

Jason Stajich jason at cgt.duhs.duke.edu
Thu May 20 08:35:51 EDT 2004

Try Bio::SearchIO,  with  'hmmer' as the format.  Alternatively
Bio::Tools::HMMER::Results should also work.  See the SearchIO HowTo for
getting started.

$hit->significance (overall significance)
$hit->raw_score (bit score)
$hit->description for the hit description.

individual hsp bit scores and evalues are available from $hsp->evalue and

On Wed, 19 May 2004, Alberto Davila wrote:

> Hi All,
> I am still looking for some help to write a parser for the "hmmsearch"
> results, would anybody have a work example to provide, please ? I am
> mainly interested to parse the e-value, bit score, and definition.
> Thanks a lot.
> Alberto
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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