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Nucleic Acids Research Advance Access published online on October 30, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn834
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© 2008 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

Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases

David M. A. Martin, Diego Miranda-Saavedra and Geoffrey J. Barton*

College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK

*To whom correspondence should be addressed. Tel: +44 1382 385860; Fax: +44 1382 385764; Email: geoff{at}compbio.dundee.ac.uk

Received August 15, 2008. Revised October 13, 2008. Accepted October 14, 2008.

The regulation of protein function through reversible phosphorylation by protein kinases and phosphatases is a general mechanism controlling virtually every cellular activity. Eukaryotic protein kinases can be classified into distinct, well-characterized groups based on amino acid sequence similarity and function. We recently reported a highly sensitive and accurate hidden Markov model-based method for the automatic detection and classification of protein kinases into these specific groups. The Kinomer v. 1.0 database presented here contains annotated classifications for the protein kinase complements of 43 eukaryotic genomes. These span the taxonomic range and include fungi (16 species), plants (6), diatoms (1), amoebas (2), protists (1) and animals (17). The kinomes are stored in a relational database and are accessible through a web interface on the basis of species, kinase group or a combination of both. In addition, the Kinomer v. 1.0 HMM library is made available for users to perform classification on arbitrary sequences. The Kinomer v. 1.0 database is a continually updated resource where direct comparison of kinase sequences across kinase groups and across species can give insights into kinase function and evolution. Kinomer v. 1.0 is available at http://www.compbio.dundee.ac.uk/kinomer/.

Present address: Diego Miranda-Saavedra, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, UK.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as the joint First Authors.


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