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

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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