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 p-values for each GO-term are computed empirically by shuffling the gene identifiers in the ranking (ensuring consistancy across species) to generate scores from the null hypothesis. Then q-values are derived from these p-values 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 q-values smaller than a specified threshold, outputting a gomo score with emprically calculated p-values and q-values for each.
Parent program: meme
MEME is a tool for discovering motifs in a group of related DNA or protein sequences. MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.