[Bioperl-l] hmmpfam

Heikki Lehvaslaiho heikki at sanbi.ac.za
Thu Jun 19 06:08:32 EDT 2008


Joonas,

I am not familiar with hmmpfam, but is is part of the HMMERtoolkit, so it 
should be possible to use Bio::SearchIO modules for parsing the output. In 
addition, it is possible to run HMMER programs directly from BioPerl (the 
bioperl-run repositoty is needed):

See:

http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/Hmmer.html
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SearchIO/hmmer.html

for code examples, and

SearchIO HOWTO
http://bio.perl.org/wiki/HOWTO%3ASearchIO

for an introduction to Bio::SearchIO.

    -Heikki

On Thursday 19 June 2008 00:52:47 Joonas Jämsen wrote:
> How to parse hmmpfam output to get gi/sequence of specified domain,
> score, E-value?
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
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