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fimo [options] <motifs> <database>


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 (in bits) into p-values, assuming a zero-order background model. The program reports all motif occurrences that have p-values smaller than the output p-value threshold. The p-value threshold can be set using the --outptu-pthresh option. The default p-value threshold is 1e-4. The p-values for each motif occurence are converted to q-values following the method of Benjamini and Hochberg ("q-value" is defined as the minimal false discovery rate at which a given motif occurrence is deemed significant). If a motif has the strand feature set to +/- (rather than +), then fimo will search both strands for occurrences.

The parameter --max-stored-scores sets the maximum number of motif occurrences that will be retained in memory. It defaults to 100,000. If the number of matches found reaches the maximum value allowed, FIMO will discard 50% of the least significant matches, and new matches falling below the significance level of the retained matches will also be discarded.

FIMO can make use of position specific priors (PSP) to improve its identification of true motif occurrences. To take advantage of PSP in FIMO you use must provide two command line options. The --psp option is used to set the name of a MEME PSP file, and the --prior-dist option is used to set the name of a file containing the binned distribution of priors.


The FASTA header lines are used as the source of sequence names. The sequence name is the string following the initial '>' up to the first white space character. If the sequence name is of the form: text:number-number, the text portion will be used as the sequence name. The numbers will be used as genomic coordinates, and the first number will be used as the coordinate of the first position of the sequence. In all other cases the coordinate of the first postion of the sequence is take as 1.


FIMO will create a directory, named fimo_out by default. Any existing output files in the directory will be overwritten. The directory will contain:

The default output directory can be overridden using the --o or --oc options which are described below.

The --text option will limit output to plain text sent to the standard output.

The HTML and plain text output contain the following columns:

The HTML and plain text output is sorted by increasing p-value.

The wiggle track output contains the following entries:

The wiggle track output is sorted by motif, sequence name, and position.