Background 1 2 3 4 5 6 7 Methodology 4 6 9 User interface Figure 1 Conclusion PMSearch is an easy-to-use and efficient tool that utilizes PFMs to predict transcription factor binding sites in DNA sequences. It offers user the flexibility to search for
putative TFBS with any set of PFMs. PMSearch outputs a plot demonstrating distribution of predicted binding sites and a table of the locations, scores, motifs and clusters of predicted binding 
sites. In addition, PMSearch provides the user access to PFMs that are relative to an input PFM for more sophisticated promoter analysis, as the predicted binding sites of one transcription 
factor could also be bond with other transcription factors that share the similar binding specificity. Such information may give hints to untangle the composite transcription regulatory network. 
We propose to update PFMs in our local dataset regularly. The source codes are available from the authors upon request.  Caveats 10