[Bioperl-l] running hmmer locally on NT

[Jason Stajich]

On Tue, 15 May 2001, Suraj Peri wrote:

> hi,
>  I have a set of Fasta format files protein sequences.
> I now want all these to be qued automatically to
> either Pfam or SMART server. Right now, in Pfam and
> SMART we have to paste only one sequence. But how can
> i automate if i have to send all the FASTA format file
> once and get the outputs in one click. 
>     Can this be done using PERL (Windows OS) . if so
> how . Please help me group!!
> Thank you
> SP
> dk
>  
I assume you are using a site like pfam.wustl.edu to query.  


One option is to automate posting queries to the Pfam
sites, but Sean has a note on the site saying that the Wustl site is
fairly overwhelmed so I don't know what your response time will be.  There
are other Pfam mirrors that you may want to use.  

If you would prefer, you will get better response time running these
queries locally by installing the hmmer software on your machine.  If you
do not have access to a UNIX machine there is are sources configured to
compile with VisualC++  as linked from the hmmer webpage (hmmer.wustl.edu)
ftp://ftp.timelogic.com/HMMER2.1/WinNTSources

As for automating the SMART queries - I've not entirely sure what of their
software is available for running locally.  You can automate submission of
jobs as we have done for submitting jobs to NCBI blast queues.  See
Bio::Tools::Run::RemoteBlast for details on that.  If you could do the
legwork to find out what one would need to do to submit and parse the
results from SMART I'm sure we'd be happy to write a module to this
effect.



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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/