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Nucleic Acids Research Advance Access originally published online on November 15, 2007
Nucleic Acids Research 2008 36(Database issue):D102-D106; doi:10.1093/nar/gkm955
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Nucleic Acids Research, 2008, Vol. 36, Database issue D102-D106
© 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.

Articles

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

Jan Christian Bryne1, Eivind Valen2, Man-Hung Eric Tang2, Troels Marstrand2, Ole Winther2,3, Isabelle da Piedade4, Anders Krogh2, Boris Lenhard1,5,* and Albin Sandelin2,*

1Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway, 2The Bioinformatics Centre, Department of Molecular Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2100 København Ø, 3Informatics and Mathematical Modeling, Building 321, Technical University of Denmark, DK-2800 Kgs. Lyngby, 4Center for Comparative Genomics, Institute of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark and 5Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway

*To whom correspondence should be addressed. Boris Lenhard: Tel: +47 55584362; Fax: +47 55584295; Email: boris.lenhard{at}bccs.uib.no Albin Sandelin: Tel: +45 52321285; Fax: +45 35325669; Email: albin{at}binf.ku.dk

Received September 14, 2007. Revised October 15, 2007. Accepted October 16, 2007.

JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database—the JASPAR CORE sub-database—has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net.

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


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