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Nucleic Acids Research, 2003, Vol. 31, No. 1 403-405
© 2003 Oxford University Press

The SBASE domain sequence library, release 10: domain architecture prediction

Kristian Vlahovicek, Laszló Kaján, János Murvai1, Zoltán Hegeds2 and Sándor Pongor*

1 ICGEB—International Center for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy 2 MSD, Inc., 131 Park Street NE, Vienna, VA 22180, USA 3 Biological Research Center of Hungarian Academy Sciences, H-6726 Szeged, Temesvári krt 62, Hungary

*To whom correspondence should be addressed. Email: pongor{at}icgeb.trieste.it

ABSTRACT

SBASE (http://www.icgeb.trieste.it/sbase) is an on-line collection of protein domain sequences and related computational tools designed to facilitate detection of domain homologies based on simple database search. The 10th ‘jubilee release’ of the SBASE library of protein domain sequences contains 1 052 904 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into over 6000 domain groups. Domain identification and functional prediction are based on a comparison of BLAST search outputs with a knowledge base of biologically significant similarities extracted from known domain groups. The knowledge base is generated automatically for each domain group from the comparison of within-group (‘self’) and out-of-group (‘non-self’) similarities. This is a memory-based approach wherein group-specific similarity functions are automatically learned from the database.


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