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.

Figure 1

Match^TM user interface maintained on the web at: http://www.gene-regulation.com/pub/programs.html#match. The left panel is used to paste the sequence (or several sequences) and to specify the name of the search. The right panel contains three major sections: matrix selection, cut-off selection and profile selection.

Figure 2

Match^TM output. (A) Tabulated result page. Every match contains: matrix ID, position of the match, strand [(+) or (−)], two scores of the match, corresponding subsequence and names of transcription factors associated with the matrix. Both the matrix ID and the factor names are hyperlinked with the corresponding TRANSFAC® entries. (B) A simple visual representation of locations of the found matches. Sites are shown above the sequence and the orientation of the ‘>’ sign corresponds to the (+) or (−) location of the sites. The results of Match^TM search is shown for the promoter of human gene for IL-12 using immune cell specific profile. Three sites that are known in this promoter (see TRANSFAC® database) were found by Match^TM (shadowed in pink) along with some new sites. Here, matrix IDs are also hyperlinked with the corresponding TRANSFAC® entries.

Figure 2

Match^TM output. (A) Tabulated result page. Every match contains: matrix ID, position of the match, strand [(+) or (−)], two scores of the match, corresponding subsequence and names of transcription factors associated with the matrix. Both the matrix ID and the factor names are hyperlinked with the corresponding TRANSFAC® entries. (B) A simple visual representation of locations of the found matches. Sites are shown above the sequence and the orientation of the ‘>’ sign corresponds to the (+) or (−) location of the sites. The results of Match^TM search is shown for the promoter of human gene for IL-12 using immune cell specific profile. Three sites that are known in this promoter (see TRANSFAC® database) were found by Match^TM (shadowed in pink) along with some new sites. Here, matrix IDs are also hyperlinked with the corresponding TRANSFAC® entries.