CentriMo takes a set of motifs and a set of equal-length DNA or RNA sequences and plots the positional distribution of the best match of each motif. The motifs are typically compendia of DNA- or RNA-binding motifs, and the sequences might be: 500 bp sequences aligned on ChIP-seq peaks or summits; 300 bp sequences centered on sets of transcription start sites or translation start sites; sequences aligned on splice-junctions; etc. CentriMo also computes the 'local enrichment' of each motif by counting the number of times its best match in each sequence occurs in a local region and applying a statistical test to see if the local enrichment is signficant. By default, CentriMo examines only regions centered, in the input sequences, but CentriMo will compute the enrichment of all regions if you specify the --local option. CentriMo uses the binomial test to compute the significance of the number of sequences where the best match occurs in a given region, assuming a uniform prior over best match positions. CentriMo reports the location and significance of the best region for each motif. CentriMo can also perform comparative enrichment, reporting the relative enrichment of the best region in a second, control set of sequences if you specify the --neg. CentriMo choses regions based on their significance in the primary set of sequences, and then it uses the Fisher exact test to evaluate the significance of the number of best matches in the region in the primary set compared with the number of best matches in the same region in the control set of sequences
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.