Smith/Waterman

[Reinhard Doelz]

Margaret Novack (novackm at NEVADA.EDU) wrote:
: MasPar Computer Corporation has a program called MPSEARCH that is an 
: implementation of the full Smith-Waterman Algorithm.

MPsrch is primarily used for rapid protein database searching on the 
MasPar Computer.  It is (C) University of Edinburgh, distributed by 
Intelligenetics Inc. and runs also on DNA sequences, as well as the 
translations. We use it happily from PC,Mac or other packages installed
on workstations or computers using our HASSLE system. 

The BLITZ server at EBI/EMBL resp. runs the software (in a previous version
as far as I know) on a MasPar as well. It it accessible by eMail.

There are other implementations of S&W on the MasPar (BLAZE by Intelligenetics
for example). 

The BIOCCELLERATOR (by Compugen Ltd.) runs Smith and Watermann, as well as 
Profile search. 

Other special hardware was / is available from vendors of sequenator machines.
 
To run S&W software on low-end machines you might refer to the 
FASTA Package by B.Pearson.  You might ask Andrew Lloyd from the 
Irish EMBnet node for more infomation and access to the software. 
He's at atlloyd at acer.gen.tcd.ie. 

regards
Reinhard Doelz
EMBnet Switzerland


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