The TRANSFAC extension can be used to search for putative transcription factor binding sites in DNA sequences. The binding site predictions are done by the Match tool, which uses the positional weight matrix library from TRANSFAC to analyze your sequences.
For each of these matrices Match contains optimized parameters, for minimization of 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 in the TRANSFAC extension, you can create your own profiles in the online version of TRANSFAC. The matrices inthe result list of the TRANSFAC extension are hyperlinked to the respective Matrix Reports in the TRANSFAC online version.
In order to be able to use the TRANSFAC extension you need a subscription to the flat file release download of TRANSFAC.