AME (Analysis of Motif Enrichment) scores a set of DNA sequences given a set of DNA-binding motifs, treating each position in the sequence as a the starting point of a possible binding event. AME supports a wide variety of methods for scoring motif enrichment, many methods of testing the scored motif enrichment for significance. By default, AME counts the number of cases where the p-value of the binding event for each motif is below a given threshold, and performs a Fisher exact test versus the number of binding events in a background sequence set to determine the p-value of the count for each motif. The background set is appended to the main sequence set in the input file, and the offset within the file where the background starts is specified on the command line.
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.