New Version 3.0 - GeneFIND Server for Protein Family Identification

Cathy Wu wu at uthct.edu
Tue Mar 31 10:07:13 EST 1998


The Bioinformatics Research Group of the University of Texas Health
Center at Tyler is pleased to announce its GeneFIND Family
Identification System available for on-line search and e-mail submission
at:

   http://diana.uthct.edu/genefind.html

GeneFIND (Gene Family Identification Network Design) is an integrated
database search system that combines several search/alignment tools and
ProClass database (http://diana.uthct.edu/proclass.html) to provide
rapid and accurate gene family classification with enriched family
information. The objectives are to improve speed and sensitivity,
differentiate global and motif similarities, and provide collective
information in an integrated platform that alleviates human annotation
effort. Multi-level filters are used, including our  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 1275 ProSite motifs (in ProSite Release 14.0, November 1997) and 3979
PIR superfamilies (in PIR Release 55.0, December 1997). This server
allows direct family identification of query sequences, and returns
search results as HTML documents showing overall global and motif scores
for likely families, BLAST scores, full-length and motif alignments, as
well as corresponding ProClass records with hypertext links to all major
family databases.

References:

- Wu, C. H., Zhao, S., Chen, H. L., Lo, C. J. and McLarty, J. (1996).
Motif identification neural design for rapid and sensitive protein
family search. CABIOS, 12, 109-118. 
- Wu, C. H., Shivakumar, S., Shivakumar, C. V. and Chen, S. (1998).
GeneFIND web server for protein family identification and information
retrieval. Bioinformatics, 14 (in press).

If you have any questions or comments, please contact me at
wu at uthct.edu.  

-- 
Cathy H. Wu, Ph.D.
Associate Professor of Biomathematics
University of Texas Health Center at Tyler
P. O. Box 2003, Tyler, TX 75710

E-Mail : wu at uthct.edu
Phone  : (903) 877-7962
Fax    : (903) 877-5914
WWW URL: http://diana.uthct.edu/~wu
GeneFIND Web Server: http://diana.uthct.edu



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