Site for searching database with user defined pattern?

Cathy Wu wuc at NBRF.Georgetown.Edu
Thu Apr 5 04:28:24 EST 2001


Hi Fergus,

You can use the "pattern search" page from our web site at:
http://pir.georgetown.edu/pirwww/search/patmatch.html

Option 2 "Search a query pattern against a sequence database" allows
you to search user-defined patterns or Prosite patterns against PIR
protein sequence database or iProClass database of PIR and Swiss-Prot
sequences.

Cathy H. Wu
Director of Bioinformatics
National Biomedical Research Foundation
Georgetown University Medical Center
3900 Reservoir Road, NW, Washington, DC 20007-2195
PIR Home: http://pir.georgetown.edu/

Fergus Doherty wrote:
> 
> Hello everybody,
> 
> I have used Pratt to generate "patterns" present in several proteins.  I
> now want to see what other proteins contain these patterns, so I need to
> yhrough them at a protein sequence database.  does anyone know of a WWW
> site that will allow me to do this?  The "patterns" are Prosite-type
> regular expressions e.g. FIL-x3-[VIL] etc, etc.
> 
> Thanks
> 
> --
> Fergus Doherty,
> School of Biomedical Sciences,
> Nottingham University,
> 
> Fergus.Doherty at nottingham.ac.uk
> 0115 970 9366 (74-41366 internal)




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