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

被引：156

作者：

Kulakovskiy, I. V. ^{[1
,7
]}

Boeva, V. A. ^{[1
,2
,3
,4
,5
]}

Favorov, A. V. ^{[1
,6
]}

Makeev, V. J. ^{[1
,7
]}

机构：

[1] Res Inst Genet & Select Ind Microorganisms, Moscow 117545, Russia

[2] Inst Curie, F-75248 Paris, France

[3] INSERM, U900, F-75248 Paris, France

[4] INSERM, U830, F-75248 Paris, France

[5] Mines ParisTech, F-77300 Fontainebleau, France

[6] Johns Hopkins Univ, Baltimore, MD 21205 USA

[7] Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia

来源：

BIOINFORMATICS | 2010年 / 26卷 / 20期

关键词：

IDENTIFICATION; DISCOVERY;

D O I：

10.1093/bioinformatics/btq488

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 ChIPSeqdata. 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.

引用

页码：2622 / 2623

页数：2

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