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Nucleic Acids Research 2006 34(Database Issue):D169-D172; doi:10.1093/nar/gkj148
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Nucleic Acids Research, 2006, Vol. 34, Database issue D169-D172
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

MIPS: analysis and annotation of proteins from whole genomes in 2005

H. W. Mewes1,2,*, D. Frishman2, K. F. X. Mayer1, M. Münsterkötter1, O. Noubibou1, P. Pagel1, T. Rattei2, M. Oesterheld1, A. Ruepp1 and V. Stümpflen1

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

*To whom correspondence should be addressed. Tel: +49 89 3187 3580; Fax: +49 89 3187 3585; Email: w.mewes{at}gsf.de

Received September 15, 2005. Revised October 28, 2005. Accepted October 28, 2005.

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).


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