P-Match: transcription factor binding site search by combining patterns and weight matrices

P-Match is a new tool for identifying transcription factor (TF) binding sites in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match is closely interconnected with the TRANSFAC database. In particular, P-Match uses the matrix library as well as sets of aligned known TF-binding sites collected in TRANSFAC and therefore provides the possibility to search for a large variety of different TF binding sites. Using results of extensive tests of recognition accuracy, we selected three sets of optimized cut-off values that minimize either false negatives or false positives, or the sum of both errors. Comparison with the weight matrix approaches such as Matchtrade mark tool shows that P-Match generally provides superior recognition accuracy in the area of low false negative errors (high sensitivity). As familiar to the user of Matchtrade mark, P-Match also allows to save user-specific profiles that include selected subsets of matrices with corresponding TF-binding sites 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 P-Match tool is available at http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi.