FIMO -- Motif search tool

The name FIMO stands for "Find Individual Motif Occurrences."

A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. Motifs are represented as position-dependent scoring matrices that describe the score of each possible letter at each position in the pattern. Individual motifs may not contain gaps. Patterns with variable-length gaps must be split into two or more separate motifs before being submitted as input to FIMO.

FIMO searches a sequence database for occurrences of known motifs, treating each motif independently. The program uses a dynamic programming algorithm to convert log-odds scores into p-values, assuming a zero-order background model. The p-values for each motif are then converted to q-values following the method of Benjamini and Hochberg (where "q-value" is defined as the minimal false discovery rate at which a given motif occurrence is deemed significant). The program reports all motif occurrences that receive q-values smaller than a specefied threshold.

FIMO takes as input a MEME output file, containing the descriptions of one or more motifs.

FIMO returns a list of matches to the motifs, sorted by p-value.