Overview

MEME-ChIP is an ensemble of tools for discovering motifs in a large set of related DNA sequences.

MEME-ChIP takes as input FASTA-formatted DNA sequences, of arbitrary size and number of sequences. It assumes that a technology has been used that results in sequences sufficiently close to centered on a likely TF binding location that it makes sense to focus on the central 100 bp portion of each sequence. ChIP-seq is an example of such a technology. The tools output the number of motifs as requested on the input form using MEME, and as many motifs as pass the threshold tests of the other tools.

Your MEME-ChIP results consist of multiple outputs in the formats described in a top-level summary file.

MEME-ChIP uses a combination of motif discovery using MEME (good for wide motifs) and DREME (good for shorter motifs) and comparison of both found motifs and the sequence data against databases of known motifs.

For more detail, see this tutorial.