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Bioinformatics. 2010 Oct 15;26(20):2622-3. doi: 10.1093/bioinformatics/btq488. Epub 2010 Aug 24.

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

Author information

1
Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia. ivan.kulakovskiy@gmail.com

Abstract

SUMMARY:

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.

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.

CONTACT:

ivan.kulakovskiy@gmail.com

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
20736340
DOI:
10.1093/bioinformatics/btq488
[Indexed for MEDLINE]
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