Regular expression scanning software

Keith Robison robison at lipid.harvard.edu
Wed Dec 14 10:37:33 EST 1994

bmb5meb at biovax.leeds.ac.uk wrote:
: Hi there,

: I'm looking for some software that runs on VMS or Unix (VMS prefered) which 
: will allow me to scan a protein database of 95000 sequences with user-defined
: regular expressions (PROSITE-like consensus sequences). Any programs will be
: considered since I need to do this reasonably soon.

Frank Kolakowski wrote a great little program called Prosearch to do this.
It was written up in Biotechniques sometime within the last year or so
(probably in a June issue).  Prosearch is an AWK program and runs on
UNIX boxes; the package comes with software to reformat Prosite into
UNIX regexp format

You might also look into James Tisdall's DNA Workbench, which is a PERL
environment for manipulating DNA and protein sequence data.  As you might
expect, it has wonderful regular expression capabilities.

The bad part is I can't remember the FTP sites!  But, if you search
these newsgroups at the BIOSCI gopher I'm sure you can find them,
or use the BIOCATALOGUE of analysis software maintained at Genethon

(indirect URL: http://golgi.harvard.edu/htbin/biopages?catalogue)

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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