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Usage:

gomo [options] <scoring file> <go-term database>

Description:

The name GOMO stands for "Gene Ontology for Motifs." The program searches in a set of ranked genes for enriched GO terms associated with high ranking genes. The genes can be ranked, for example by applying a motif scoring algorithms on their upstream sequence. The E-values for each GO-term are computed and q-values are provided as well, following the method of Benjamini and Hochberg (where "q-value" is defined as the minimal false discovery rate at which a given GO-term is deemed significant). The program reports all GO terms that receive E-values smaller than a specified threshold.

Input:

Output:

GOMO will create a directory, named gomo_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.

Options: