An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale

An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale
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用于在基因组规模上准确预测和分析顺式调控基序的集成工具包

DOI：
10.1093/bioinformatics/btt397
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发表时间：
2013-09-15
期刊：
BIOINFORMATICS
影响因子：
5.8
通讯作者：
Xu, Ying
Xu, Ying
中科院分区：
生物学3区
文献类型：
--
作者：
Ma, Qin;Liu, Bingqiang;Xu, Ying

文献摘要

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动机 我们提供了一个集成的工具包BoBro2.0，用于预测和分析顺式调控基序。该工具包可以(I)可靠地在基因组水平上识别具有统计意义的顺式调控基序；(Ii)使用一种新的P值估计方法准确地扫描指定基因组区域中查询基序的所有基序实例；(Iii)提供高度可靠的识别基序的比较和聚类，这考虑到来自基序侧翼区域的微弱信号；以及(Iv)分析调控区域中的共生基序。 结果 我们用BoBro2.0和Meme包对基序预测进行了系统的比较。在大肠杆菌K12基因组和人类基因组上的比较结果表明，BoBro2.0能够更有效地识别基因组尺度上有统计意义的基序，更准确地识别基序实例，并得到比Meme更可靠的基序簇。此外，BoBro2.0还提供了已识别基序之间的相关性分析，以便于推断转录因子的联合调控关系。 可用性 该程序的源代码可在http://code.google.com/p/bobro/.上免费获得，供非商业用途使用 接触 邮箱：xyn@bmb.uga.edu 补充信息 补充数据可在生物信息学在线上获得。
MOTIVATION We present an integrated toolkit, BoBro2.0, for prediction and analysis of cis-regulatory motifs. This toolkit can (i) reliably identify statistically significant cis-regulatory motifs at a genome scale; (ii) accurately scan for all motif instances of a query motif in specified genomic regions using a novel method for P-value estimation; (iii) provide highly reliable comparisons and clustering of identified motifs, which takes into consideration the weak signals from the flanking regions of the motifs; and (iv) analyze co-occurring motifs in the regulatory regions. RESULTS We have carried out systematic comparisons between motif predictions using BoBro2.0 and the MEME package. The comparison results on Escherichia coli K12 genome and the human genome show that BoBro2.0 can identify the statistically significant motifs at a genome scale more efficiently, identify motif instances more accurately and get more reliable motif clusters than MEME. In addition, BoBro2.0 provides correlational analyses among the identified motifs to facilitate the inference of joint regulation relationships of transcription factors. AVAILABILITY The source code of the program is freely available for noncommercial uses at http://code.google.com/p/bobro/. CONTACT xyn@bmb.uga.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.