ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster.
Ivan Kulakovskiy ( ivan-dot-kulakovskiy-wow-gmail-dot-com)
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Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ
Deep and wide digging for binding motifs in ChIP-Seq data.
Bioinformatics 2010 Oct 15;26(20):2622-3. Epub 2010 Aug 24