Nucleic Acids Research, 2003, Vol. 31, No. 13 3576-3579
© 2003 Oxford University Press
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
1 BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany 2 Institute of Cytology and Genetics, Pr. Lavrentyeva 10, 360090, Novosibirsk, Russia 3 Department of Bioinformatics, UKG, University of Göttingen, Goldschmidtstr. 1, D-37077 Göttingen, Germany
*To whom correpondence should be addressed at BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany. Tel: +49 5331 858441; Fax: +49 5331 858470; Email: ake{at}biobase.de
MatchTM is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. MatchTM is closely interconnected and distributed together with the TRANSFAC® database. In particular, MatchTM uses the matrix library collected in TRANSFAC® and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC® team. A public version of the MatchTM tool is available at: http://www.gene-regulation.com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called MatchTM Professional is available at http://www.biobase.de.
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C. Zhang, Z. Xuan, S. Otto, J. R. Hover, S. R. McCorkle, G. Mandel, and M. Q. Zhang A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res., January 1, 2006; 34(8): 2238 - 2246. [Abstract] [Full Text] [PDF]
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S. K. Kummerfeld and S. A. Teichmann DBD: a transcription factor prediction database Nucleic Acids Res., January 1, 2006; 34(suppl_1): D74 - D81. [Abstract] [Full Text] [PDF]
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A. A. Sharov, D. B. Dudekula, and M. S. H. Ko CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome DNA Res, January 1, 2006; 13(3): 123 - 134. [Abstract] [Full Text] [PDF]
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