DEME ( Discriminatively Enhanced Motif Elicitation) is a discriminative motif discovery algorithm that searches for overrepresented sequence patterns in a set of unaligned sequences relative to another set of sequences. DEME may be used to search either DNA or protein sequences. In fact, DEME can be applied to any motif discovery problem where sequences can be assigned to a "positive" set or a "negative" set, where the positive set contains sequences that are believed to contain the motif of interest and the negative set is assumed not to contain the motif. Examples of applications for DEME include identifying short linear motifs (SLiMs) in sets of peptides, discovering transcription factor binding site motifs in ChIP-chip data (using probe sequences enriched for binding as the positive set and non-binding probe sequences as the negative set) or finding protein motifs involved in thermal stability using sets of orthologous proteins from thermophilic and mesophilic organisms.
Download the Linux and OSX executables here.