Consensus pattern searching

G.J. Barton mbgjb at s-crim1.dl.ac.uk
Thu Sep 15 07:06:45 EST 1994


In article <351the$6tj at u.cc.utah.edu>, Tom Doak <tom_doak at hlthsci.med.utah.edu> writes:
|> In article <1994Sep12.100417.9727 at leeds.ac.uk> ,
|> bmb5meb at biovax.leeds.ac.uk writes:
|> 
|> >I am looking for a program that will run on a DEC Vax running VAX/VMS
|> v5.5-2
|> >or a DEC Alpha running OpenVMS AXP v1.5 which will allow me to scan a
|> protein
|> >database with consensus patterns. Preferably the program should allow 
|> >patterns with flexible gaps, etc., and needs to be able to handle a
|> database
|> >which contains ~85,000 sequences. Please post or e-mail any suggestions;
|> any
|> >help will be greatly appreciated.
|> >
|> >Mike.
|> >

You might like to try the AMPS package.  This includes "flexible pattern
scanning" which may do what you want.  In fact, this is a combination of 
Gribskov-style "profiles" and patterns with specified gap-ranges.
(See Barton & Sternberg, 1990,
"Flexible protein sequence patterns, a sensitive method to detect weak structural 
similarities", J. Mol. Biol, 212, 389-402.).

AMPS is available from our ftp/WWW servers.  Read the README file for
instructions.  The programs were originally developed under VAX/VMS, though I only
support Unix now.  Porting back to VMS should be straightforward - full sources
are included for academic use.

Geoff. Barton

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Dr. Geoffrey J. Barton
Laboratory of Molecular Biophysics, University of Oxford
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.

email:  gjb at bioch.ox.ac.uk    Telephone: +44 865 275368    Fax: +44 865 510454 
anonymous-ftp: geoff.biop.ox.ac.uk             WWW: http://geoff.biop.ox.ac.uk
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