MCAST searches a sequence database for statistically significant clusters of non-overlapping occurrences of a given set of motifs. A motif 'hit' is a sequence position that is sufficiently similar to a motif in the query, where the score for a motif at a particular sequence position is computed without gaps. To compute the p-value of a motif score, MCAST assumes that the sequences in the database were generated by a 0-order Markov process (see option --bgfile, below). To be considered a hit, the p-value of the motif alignment score must be less than the significance threshold, pthresh (see option --motif-pthresh, below). Note that MCAST searches for hits on both strands of the sequences. A cluster of non-overlapping hits is called a 'match'. The user specifies the maximum allowed distance between the hits in a match using the --max-gap option. Two hits separated by more than the maximum allowed gap will be reported in separate matches.
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.