The SYSTERS Protein Family Database in 2005

Thomas Meinel; Antje Krause; Hannes Luz; Martin Vingron; Eike Staub

doi:10.1093/nar/gki030

The SYSTERS Protein Family Database in 2005

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D226-9. doi: 10.1093/nar/gki030.

Authors

Thomas Meinel¹, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub

Affiliation

¹ Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Databases, Protein*
Phylogeny
Proteins / classification*
Sequence Analysis, Protein*
Software
User-Computer Interface

Substances

Proteins