fimo [options] <motifs> <database>

Description:

The name fimo stands for "Find Individual Motif Occurences." The program 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 program reports all motif occurrences that receive p-values smaller than a specified threshold. If a given motif has the strand feature set to +/- (rather than +), then fimo will search both strands for occurrences.

Input:

• <motifs> is a list of motifs, in MEME format.
• <database> is a collection of sequences in FASTA format.

Output:

An XML file using the CisML schema.