Nucleic Acids Research, 2005, Vol. 33, Database issue D226-D229
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The SYSTERS Protein Family Database in 2005
Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin, Germany and 1 TFH Wildau, Biosystemtechnik/Bioinformatik, Bahnhofstrasse, 15745 Wildau, Germany
* To whom correspondence should be addressed. Tel: +49 30 8413 1147; Fax: +49 30 8413 1152; Email: Eike.Staub{at}molgen.mpg.de
Received September 13, 2004; Revised and Accepted September 22, 2004
The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. The SYSTERS web server (http://systers.molgen.mpg.de) provides access to 158 153 SYSTERS protein families. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes.
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