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Nucleic Acids Research Advance Access published online on November 23, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm963
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SIMAP—structuring the network of protein similarities

Thomas Rattei1,*, Patrick Tischler1, Roland Arnold1, Franz Hamberger1, Jörg Krebs1, Jan Krumsiek1, Benedikt Wachinger1, Volker Stümpflen2 and Werner Mewes1,2

1Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Technische Universität München, 85350 Freising-Weihenstephan, Germany and 2Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany

*To whom correspondence should be addressed. Tel: +49 8161 712132; Fax: +49 8161 712186; Email: t.rattei{at}wzw.tum.de

Received September 14, 2007. Revised October 17, 2007. Accepted October 17, 2007.

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 ~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.


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