SIMAP--structuring the network of protein similarities.
Protein sequences are the most important source of evolutionary and functional information for new proteins. In order to facilitate the computationally intensive tasks of sequence analysis, the Similarity Matrix of Proteins (SIMAP) database aims to provide a comprehensive and up-to-date dataset of the pre-calculated sequence similarity matrix and sequence-based features like InterPro domains for all proteins contained in the major public sequence databases. As of September 2007, SIMAP covers approximately 17 million proteins and more than 6 million non-redundant sequences and provides a complete annotation based on InterPro 16. Novel features of SIMAP include a new, portlet-based web portal providing multiple, structured views on retrieved proteins and integration of protein clusters and a unique search method for similar domain architectures. Access to SIMAP is freely provided for academic use through the web portal for individuals at http://mips.gsf.de/simap/and through Web Services for programmatic access at http://mips.gsf.de/webservices/services/SimapService2.0?wsdl.
Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Technische Universität München, 85350 Freising-Weihenstephan, Germany.
Thomas
T
Rattei
Patrick
P
Tischler
Roland
R
Arnold
Franz
F
Hamberger
Jörg
J
Krebs
Jan
J
Krumsiek
Benedikt
B
Wachinger
Volker
V
Stümpflen
Werner
W
Mewes
D030562:Databases, Protein; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
D011506:Proteins