Nucleic Acids Research, 2005, Vol. 33, Database issue D223-D225
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
ekICGEB–International Center for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy and 1 Bioinformatics Group, Biological Research Center of Hungarian Academy Sciences, H-6726 Szeged, Temesvári krt 62, Hungary
* To whom correspondence should be addressed. Tel: +39 040 3757300; Fax: +39 040 226 555; Email: pongor{at}icgeb.org
Received September 14, 2004; Revised and Accepted October 18, 2004
SBASE (http://www.icgeb.trieste.it/sbase) is an online resource designed to facilitate the detection of domain homologies based on sequence database search. The present release of the SBASE A library of protein domain sequences contains 972 397 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into 8547 domain groups. SBASE B contains 169 916 domain sequences clustered into 2526 less well-characterized groups. Domain prediction is based on an evaluation of database search results in comparison with a ‘similarity network’ of inter-sequence similarity scores, using support vector machines trained on similarity search results of known domains.
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