New Release 2.0 - ProClass Protein Family Database

Cathy Wu wu at uthct.edu
Thu Dec 4 09:56:49 EST 1997

The Bioinformatics Research Group of the University of Texas Health
Center at Tyler is pleased to announce the Release 2.0 of its
ProClass Protein Family Database.  The database is available for
on-line search at:


Free copies of the ProClass Database and its query program can be
obtained via anonymous FTP to:


The ProClass Protein Family Database, cited in a recent Science
Genome issue (Vol. 278, No. 5338, p. 615, Genome Maps), is a
non-redundant database organized according to family relationships
as defined collectively by PIR superfamilies and ProSite patterns.
The objectives are to facilitate protein family information
retrieval, unveil domain and family relationships, and classify
multi-domained proteins. This is achieved by combining global
and motif sequence similarities into a single classification scheme.
The current ProClass release consists of 103,312 sequence entries
retrieved from PIR-international (Release 54.0, September 1997) and
SwissProt (Release 34.0, November 1996) 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.

Major features of ProClass Release 2.0 are:

- Compilation of ProClass_Motif.  The data set provides an up-to-date
  and comprehensive source of motif sequences and alignments for all
  ProSite patterns.  Included are several thousands of new family
  members which are not catalogued in ProSite (Release 13.0), but
  identified by our GeneFIND family identification system (version
  2.0, December 1997, http://diana.uthct.edu/genefind.html).

- Hypertext links to all major family databases.  Included are links
  to the underlying raw databases (PIR, SwissProt and ProSite), 
  family/superfamily alignments (PIR_ALN, MIPS), other family/domain
  databases (BLOCKS, PRINTS, ProDom, Pfam), and structural class
  databases (SCOP, CATH, HSSP). 

- Wu, C. H., Zhao, S. and Chen, H. L. (1996). A protein class
  database organized with ProSite protein groups and PIR 
  superfamilies. Journal of Computational Biology, 3(4), 547-561.
- Wu, C. H. and Shivakumar, S. (1998). ProClass protein family 
  database: New version with motif alignments. Proceedings of the
  Pacific Symposium on Biocomputing '98, (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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