MATLIGN: a motif clustering, comparison and matching tool

Background: Sequence motifs representing transcription factor binding sites (TFBS) are commonly encoded as position frequency matrices (PFM) or degenerate consensus sequences (CS). These formats are used to represent the characterised TFBS profiles stored in transcription factor databases, as well as to represent the potential motifs predicted using computational methods. To fill the gap between the known and predicted motifs, methods are needed for the post-processing of prediction results, i.e. for matching, comparison and clustering of pre-selected motifs. The computational identification of over-represented motifs in sets of DNA sequences is, in particular, a task where post-processing can dramatically simplify the analysis. Efficient postprocessing, for example, reduces the redundancy of the motifs predicted and enables them to be annotated. Results: In order to facilitate the post-processing of motifs, in both PFM and CS formats, we have developed a tool called Matlign. The tool...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Matti Kankainen, Ari Löytynoja
• Keywords: BMCBI 2007, Potential Motifs, Sequence Motifs, Transcription Factor