Deep and wide digging for binding motifs in ChIP-Seq data.
CONCLUSIONS
ChIP-Seq data are 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 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 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.


METHODS
ChIPMunk is freely available within the ru_genetika Java package: http://line.imb.ac.ru/ChIPMunk. Web-based version is also available.


BACKGROUND
ivan.kulakovskiy@gmail.com


BACKGROUND
Supplementary data are available at Bioinformatics online.
Kulakovskiy
I V
IV
Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia. ivan.kulakovskiy@gmail.com
Boeva
V A
VA
Favorov
A V
AV
Makeev
V J
VJ
D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D016208:Databases, Factual; D017422:Sequence Analysis, DNA / Q000379:methods*
D004247:DNA