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New Release 4.1 - ProClass Database and GeneFIND System

Cathy Wu wuc at NBRF.GEORGETOWN.EDU
Tue May 11 08:50:41 EST 1999


New release 4.1 of the ProClass Protein Family Database and the
GeneFIND Family Identification System are now accessible from a new
WWW site at: 

   http://pir.georgetown.edu/gfserver/

Direct on-line searches are available at:

   http://pir.georgetown.edu/gfserver/proclass.html (ProClass)
   http://pir.georgetown.edu/gfserver/genefind.html (GeneFIND)

The ProClass Protein Family Database is a non-redundant database
organized according to family relationships as defined collectively by
PIR superfamilies and ProSite motif patterns.  The current ProClass
release consists of 138,004 annotated sequence entries retrieved from
PIR-international (Release 60.0, March 1999) and SwissProt (Release
37.0, December 1998) databases.  It has three sub-databases,
ProClass_Family (PCFam), ProClass_Sequence (PCSeq) and ProClass_Motif
(PCMotif) for the collections of family, sequence and motif entries. 
ProClass has hypertext links to all major family/domain and structural
class databases. 

GeneFIND (Gene Family Identification Network Design) is an integrated
database search system that provides rapid and accurate protein family
classification using multi-level filters, including MOTIFIND neural
networks, BLAST search, SSEARCH (Smith-Waterman) sequence alignment,
motif pattern matching, hidden Markov motif modeling and ClustalW
multiple motif alignment.  The current GeneFIND implementation
provides full-scale identification of more than 1200 ProSite protein
groups and more than 6000 PIR superfamilies.  The on-line server
allows direct family identification of query sequences, and returns
search results showing overall global and motif scores of likely
families, BLAST scores, full-length and motif alignments, as well as
corresponding ProClass records with hypertext links.

References:

- Wu, Cathy, S. Shivakumar and H. Huang. (1999). ProClass protein
family database. Nucleic Acids Research, 27 (1), 272-274.
- Wu, Cathy, S. Shivakumar, C. V. Shivakumar and S. Chen. (1998).
GeneFIND web server for protein family identification and information
retrieval. Bioinformatics, 14 (2), 223-224.

Please contact Cathy Wu at wuc at nbrf.georgetown.edu for any comments,
and for inquiries regarding obtaining copies of the ProClass database
or GeneFIND program, or setting up mirror sites or links.




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