MATCHTM: a tool for searching transcription factor binding sites in DNA sequences.
Kel, A.E. 1,2,*; Goling, E. 1[latin sharp s]; Reuter, I. 1; Cheremushkin, E. 2; Kel-Margoulis, O.V. 1,2; Wingender, E. 1,3
[Article] Nucleic Acids Research. 31(13):3576-3579, July 1, 2003.

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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(R) database. In particular, MatchTM uses the matrix library collected in TRANSFAC(R) 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(R) 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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