Pmp_bf calculates the statistical power of a phylogenetic motif model. Phylogenetic motif models extend the popular position weight matrix (PWM) motif models used in computational biology to represent and identify sequence features such as TF binding sites (TFBSs), splice junctions and binding domains in DNA, RNA and protein molecules, respectively. Whereas a PWM computes the probability of given region in a single genome being an instance of a motif, a PMM computes the probability of an ungapped region in a multiple alignment being comprised of instances of the motif that evolved independently from an ancestral instance.
Parent program: meme
MEME is a tool for discovering motifs in a group of related DNA or protein sequences. MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.