Match is a powerful web-based tool, which identifies transcription factor binding sites in DNA sequences by weight matrix search. Match is integrated in TRANSFAC Professional and uses its positional weight matrices for analysis.
For each of these matrices Match contains optimized parameters, which minimize the error rates (false negative rate and false positive rate).
As a special feature, Match provides the option to use profiles, which are specific subsets of matrices with optimized cut-offs. These profiles allow users to adapt Match to their specific interests. For example, promoters of a certain tissue can be searched with tissue specific profiles. In addition to several pre-defined profiles provided by Match™, the user can create his own profiles with the Match Profiler tool.
The Match results, which can be viewed in tabular form or in a graphical representation, are linked to the corresponding matrix and transcription factor entries in TRANSFAC Professional.
In addition to using the matrices from TRANSFAC Professional, the user can create his own matrices from a set of aligned binding sites on the Matrix Generation page. These user-created matrices can be included in Match searches.
The matrices used to identify a binding site are listed, as well as the position and strand where the site was found, the scores of the match between site and sequence (1.0 means 100% similarity), the nucleotide sequence of the matching sites and the names of the potential binding factors.
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