[1] 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.
DREME is computationally efficient and therefore is suitable for motif search on large data sets derived from ChIP-seq (Chromatin immunoprecipitation followed by sequencing) experiments.
MEME-ChIP is a tool for discovering motifs in data sets derived from ChIP-seq (Chromatin immunoprecipitation followed by sequencing) experiments.
[7] Central Motif Enrichment Analysis (CentriMo) is a tool for inferring direct DNA binding from ChIP-seq data.
CentriMo takes a set of sequences and plots the occurrence of motifs relative to the ChIP-seq peak.