FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
fimo [options] <motifs> <database>
Specify the source of a background model for converting a frequency matrix to a log-odds score matrix and for use in estimating the p-values of match scores. The value of file is either the path to a file in Markov Background Model Format, or one of the keywords motif-file, --motif-- or --uniform--. The first two keywords cause the 0-order letter frequencies contained in the motif file to be used, and --uniform-- causes uniform letter frequencies to be used.
If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random.
Set the maximum number of scores that will be stored. Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate.
Use only the motif identified by id. This option may be repeated.
A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency
Do not compute a q-value for each p-value. The q-value calculation is that of Benjamini and Hochberg
Do not score the reverse complement DNA strand.
Create a folder called dir and write output files in it. This option is not compatible with --oc as only one output folder is allowed.
Create a folder called dir but if it already exists allow overwriting the contents. This option is not compatible with --o as only one output folder is allowed.
When this option is specified each sequence header will be checked for UCSC style genomic coordinates.
File containing position specific priors (PSP) in MEME PSP format or wiggle format. This file can be generated using the create-priors utility.
The alpha parameter for calculating position specific priors, used in conjuction with the psp option. Alpha represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest. Alpha must be between 0 and 1.
File containing binned distribution of priors. This file can be generated using the create-priors utility.
Directs the program to use q-values for the output threshold.
Like the --text option, this limits output to plain text sent to standard out, but in addition, turns off output of the sequence of motif matches. This speeds up processing considerably.
Limits output to plain text sent to standard out. For FIMO, the text output is unsorted, and q-values are not reported. This mode allows the program to search an arbitrarily large database, because results are not stored in memory.
The output threshold for displaying search results. Only search results with a p-value less than the threshold will be output. The threshold can be set to use q-values rather than p-values via the --qv-thresh option.
A number that regulates the verbosity level of the output information messages. If set to 1 (quiet) then it will only output error messages whereas the other extreme 5 (dump) outputs lots of mostly useless information.
Display the version and exit.