[Bioperl-l] What is MPsrch?

[Yee Man]

Thanks for your reply. How does it compare to ssearch? ssearch is using
Phil Green's algorithm which is a SW algorithm with a little heuristic.
How "true" is the SW in MPsrch?

I remember Aaron Mackey says he also has a MP version of ssearch. How does
that one compare with MPsrch?

Thanks
Yee Man

On 16 Apr 2003, Heikki Lehvaslaiho wrote:

> Yes.
> 
> In the side bar, link "MPsrch Help":
> 
> "MPsrch is a biological protein sequence comparison tool that implements
> the true Smith and Waterman algorithm. It runs a search on a HP/COMPAQ
> cluster, a family of massively parallel computers. It allows an
> exhaustive search in a reasonable computational time. MPsrch utilises an
> exhaustive algorithm, which is recognised as the most sensitive sequence
> comparison method available, whereas Blast utilises a heuristic one,
> which speeds up searches by reducing the complexity of the problem. As a
> consequence, MPsrch is capable of identifying hits in cases where Blast
> fails with fewer false hits."
>  
> 	-Heikki
> 
> On Tue, 2003-04-15 at 18:25, Yee Man wrote:
> > Hi
> > 
> > 	I was reading a Comparative Genomics book written by Koonin &
> > Galperin (both NCBI scientists). They mentioned an EBI program called
> > MPsrch that does fast Smith-Waterman.
> > http://www.ebi.ac.uk/MPsrch/
> > 
> > 	Is this just an multi-processor implemention of ssearch?
> > 
> > Thanks
> > Yee Man
> > 
> > _______________________________________________
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> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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