1 Deep and wide digging for binding motifs in ChIP-Seq data

Summary: ChIP-Seq data is a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for motif discovery in ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require trunca-tion 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. Availability and Implementation: ChIPMunk is freely available within the ru_genetika Java package:http://line.imb.ac.ru/ChIPMunk. Web-based version is also available. Supplementary information