Patch is a web-based tool integrated in TRANSFAC Professional, which identifies transcription factor binding sites by pattern matching. The transcription factor binding sites of TRANSFAC Professional are used as search patterns.
To restrict the search, the user can specify the maximum number of mismatching nucleotides in a match between search pattern and sequence and he can specify the penalty for a mismatch. Using the powerful search engine of TRANSFAC Professional, the user can collect his own sets of binding sites and use them directly for an analysis with Patch. In addition, Patch provides several predefined site sets.
The results of Patch can be viewed in both tabular and graphical representation. The binding sites found are linked to the corresponding entries in TRANSFAC Professional.
The name of the binding site, the position and strand where the sites were found, the number of mismatching nucleotides, the score of the matching site (100 means 100% identity), the potential binding factors and the search patterns are listed.
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