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Nucleic Acids Research, 2000, Vol. 28, No. 1 273-276
© 2000 Oxford University Press

ProClass protein family database

Hongzhan Huang, Chunlin Xiao and Cathy H. Wu*

Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of >155 000 sequence entries retrieved from both PIR-International and SWISS-PROT databases. Approximately 92 000 or 60% of the ProClass entries are classified into ~6000 families, including a large number of new members detected by our GeneFIND family identification system. The ProClass motif collection contains ~72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including >21 000 matches not listed in PROSITE and mostly detected from unique PIR sequences. To maximize family information retrieval, the database provides links to various protein family, domain, alignment and structural class databases. With its high classification rate and comprehensive family relationships, ProClass can be used to support full-scale genomic annotation. The database, now being implemented in an object-relational database management system, is available for online sequence search and record retrieval from our WWW server at http://pir.georgetown.edu/gfserver/ proclass.html

* To whom correspondence should be addressed. Tel: +1 202 687 2121; Fax: +1 202 687 1662; Email: wuc@nbrf.georgetown.edu


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