深度和广泛挖掘 ChIP-Seq 数据中的结合基序。

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

机构信息

Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russia.

出版信息

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

DOI:10.1093/bioinformatics/btq488

PMID:20736340

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.

摘要

ChIP-Seq 数据对基序发现来说是一个新的挑战。这样的数据通常由数千个具有碱基特异性覆盖值的 DNA 片段组成。我们提出了我们的 DNA 基序发现软件 ChIPMunk 的新版本，该版本适用于 ChIP-Seq 数据。ChIPMunk 是一种迭代算法，它将贪婪优化与引导相结合，并使用覆盖图作为基序位置偏好。ChIPMunk 不需要截断长的 DNA 片段，对于处理多达数万条数据序列来说是实用的。与传统的（MEME）或面向 ChIP-Seq 的（HMS）基序发现工具的比较表明，ChIPMunk 可以以相同或更好的质量识别正确的基序，但速度快得多。