MATLIGN: a motif clustering, comparison and matching tool.

ABSTRACT:

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 post-processing, for example, reduces the re

SUBMITTER: Kankainen M 

PROVIDER: S-EPMC1925120 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature