[Bioperl-l] hmmpfam

Sendu Bala bix at sendu.me.uk
Thu Jun 19 06:44:43 EDT 2008


Heikki Lehvaslaiho wrote:
> 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

You may also prefer hmmer_pull:
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SearchIO/hmmer_pull.html
Which is faster and might behave more like you expect.


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