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Nucleic Acids Research Advance Access published online on October 21, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn749
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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

PEDANT covers all complete RefSeq genomes

Mathias C. Walter1, Thomas Rattei2, Roland Arnold2, Ulrich Güldener1, Martin Münsterkötter1, Karamfilka Nenova1, Gabi Kastenmüller1, Patrick Tischler2, Andreas Wölling3, Andreas Volz3, Norbert Pongratz3, Ralf Jost3, Hans-Werner Mewes1,2 and Dmitrij Frishman1,2,*

1Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, 2Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, 85350 Freising and 3Biomax Informatics AG, Lochhamer Strasse 9, 82152 Martinsried, Germany

*To whom correspondence should be addressed. Tel: +49 8161 712134; Fax: +49 8161 712186; Email: d.frishman{at}wzw.tum.de

Received September 15, 2008. Accepted October 3, 2008.

The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.


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