Introduction to Match, FMatch and Composite Model Search


Match, and the alternative Composite Model search, is a multi-component BKL Tool that is designed for predicting transcription factor binding sites in a DNA sequence of interest, using mononucleotide weight matrices from TRANSFAC.

The tool allows you to specify your search by using profiles (for Match) or models (for Composite Model).

Please note: We use the term "profile" for a specific subset of weight matrices from the TRANSFAC library with core similarity cut-off values and matrix similarity cut-off values for each matrix. We use the term "model" for pairs of linked matrices with matrix similarity cut-off values for each matrix.

In addition, tools are provided that enable researchers to create custom profiles, matrices or models:

  • The Profile Generation tool allows user to create custom profiles. The matrices to be included in the profile can either be directly selected in the Profile Generation tool, or with the function in the database search engine, a profile can be generated including matrices for factors with certain tissue specificity or other properties.

  • The Matrix Generation tool enables researchers to create matrices from a set of aligned sequences. Optimized cut-off values are estimated for these matrices. After they have been included in a profile with the help of the Profile Generation tool, they can be used for a search in Match.

  • The Composite Model Editor tool enables researchers to create models using matrices within the TRANSFAC matrix library or which have been uploaded by the user.

Searching for Transcription Factor Binding Sites with Match, FMatch and Composite Model

Instructions for using Match, FMatch and Composite Model to search for transcription factor binding sites are provided here.

Creating Profiles with the Profile Generation Tool

Instructions for using the Profile Generation tool to create custom profiles are provided here. Information on how to "Create Match Profiles" based on a database search result are provided here.

Creating Matrices with the Matrix Generation Tool

Instructions for using Matrix Generation tool to create matrices are provided here.

Please note: From release to release, results obtained with MatchTM can change, due to the addition of new matrices, matrix and profile updates, and improved cut-offs. Therefore, please always note the release / version number of TRANSFAC® Professional / MatchTM which you used for your analysis. Although we advise to use always the latest release of TRANSFAC® Professional, in case you are doing a large analysis for which you want to assure that the conditions stay constant, it is advisable to do the whole analysis with one and the same locally installed version.

Creating Models with the Composite Model Editor Tool

Instructions for using the Composite Model Editor tool to create models are provided here.


Kel, A. E.; Gößling, E.; Reuter, I.; Cheremushkin, E.; Kel-Margoulis, O. V.; Wingender, E. (2003) "MATCH: A tool for searching transcription factor binding sites in DNA sequences" Nucleic Acids Res. 31, 3576-3579. [Abstract]

Additionally, please refer to BIOBASE as the creator of this tool.


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