MATCH™: A tool for searching transcription factor binding sites in DNA sequences

Abstract

Match™ is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match™ is closely interconnected and distributed together with the TRANSFAC® database. In particular, Match™ 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 Match™ 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 Match™ Professional is available at http://www.biobase.de.