SBASE

http://www.icgeb.trieste.it/sbase

Vlahovicek, K.¹, Murvai, J.¹, Barta, E.², Pongor, S.¹

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

Contact pongor@icgeb.trieste.it

Database Description

SBASE is an on-line resource of protein domain sequences designed to facilitate detection of domain homologies based on simple database search. The ninth release of the SBASE library of protein domain sequences contains 320 thousand 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. Communications of the ACM, 29:1213-1228, 1986). <http://www.icgeb.trieste.it/sbase/> <http://sbase.abc.hu/sbase/>.

Recent Developments

i) Release 9.0 contains over 320 thousand sequence entries, 11% more than release 8.0. The entries are now separated into two large groups, DOMAIN and PROTEIN FAMILY. The latter are indicated by the word FAMILY in the standard name (SN) line of the records. ii) The statistical description of the domain groups is now available via the web server. The layout of the web server has changed. iii) A relational database architecture (SQL) is used for producing and maintaining the data. This makes it possible to keep permanent accession codes and, for the servers, to process BLAST searches and statistics more rapidly. iv) The domain prediction system has been complemented with a new, faster boundary prediction scheme that has a graphic output

Acknowledgements

This work was supported in part by EMBnet, the European Molecular Biology Network in the framework of EU grant ERBBIO4-CT96-0030. SBASE was established in 1990 and is maintained collaboratively by the International Center for Genetic Engineering and Biotechnology, Trieste, Italy and the Agricultural Biotechnology Center, Gˆdˆllˆ, Hungary.