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Nucleic Acids Research, 2002, Vol. 30, No. 1 273-275
© 2002 Oxford University Press

The SBASE protein domain library, release 9.0: an online resource for protein domain identification

Kristian Vlahovicek1, János Murvai1, Endre Barta2 and Sándor Pongor1,2,*

1International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy and 2Agricultural Biotechnology Center, 2100 Gödöllö, Hungary

SBASE (http://www.icgeb.trieste.it/sbase) is an online resource of protein domain sequences designed to facilitate detection of domain homologies based on a simple database search. The ninth release of the SBASE library of protein domain sequences contains 320 000 annotated structural, functional, ligand-binding and topogenic segments of proteins clustered into over 3481 domain groups and 483 protein families. Domain identification and functional prediction are based on a comparison of BLAST search outputs with a knowledge base of within-group (‘self’) and out-of-group (‘non-self’) similarities of the known domain groups. This is a memory-based approach wherein class-specific similarity functions are automatically learned from the database [Stanfill,C. and Waltz,D. (1986) Commun. ACM, 29, 1213–1228].

* To whom correspondence should be addressed at: International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. Tel: +39 040 3757300; Fax: +39 226 555; Email: pongor{at}icgeb.trieste.it Present address: János Murvai, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA


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