AMA stands for 'Average Motif Affinity'. The program scores a set of DNA sequences given a DNA-binding motif, treating each position in the sequence as a possible binding event. The score is calculated by averaging the likelihood ratio scores for all feasible binding events to the given sequence and to its reverse strand. The binding strength at each potential site is defined as the likelihood ratio of the site under the motif versus under a zero-order background model provided by the user. By default, AMA reports the average motif affinity score. It can also report p-values, which are estimated analytically using the given zero-order background model or using the GC-content of each sequence. AMA can also compute the sequence-dependent likelihood ratio score used by Clover. The denominator of this score depends on the sequence being scored, and is the likelihood of the site under a Markov model derived from the sequence itself. Unlike Clover, AMA also allows higher-order sequence-derived Markov models (see --sdbg option below).
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.