DME (Discriminating Motif Enumerator) is a program that discovers transcription factor binding site motifs in nucleotide sequences. DME identifies motifs, represented as position weight matrices, that are overrepresented in one set of sequences relative to another set. The ability to directly optimize relative overrepresentation is a unique feature of DME, making DME an ideal tool for analyzing promoters of transcripts found to have differential expression in a particular context. The optimization procedure is based on an enumerative algorithm that is guaranteed to identify optimal motifs from a discrete space of matrices with a specific lower bound on information content. This strategy scales very well with the number and length of the sequences used, and is well-suited to analyzing very large data sets.
Bioinformatics. 2007 Jan 1;23(1):21-9. Epub 2006 Oct 18.
Computational prediction of novel components of lung transcriptional networks.
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS.