A new framework for identifying cis-regulatory motifs in prokaryotes.
A new framework for identifying cis-regulatory motifs in prokaryotes.
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识别原核生物顺式调控基序的新框架
DOI：
10.1093/nar/gkq948
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发表时间：
2011-04
影响因子：
14.9
通讯作者：
Xu Y
中科院分区：
文献类型：
--
作者：
Li G;Liu B;Ma Q;Xu Y
我们提出了一种新的算法，BOBRO，预测在一组给定的启动子序列的顺式调控基序。该算法大大提高了预测精度，并基于两个关键的新思想扩展了现有程序的适用范围：（i）我们开发了一种非常有效的方法，用于可靠地评估给定启动子中每个位置成为启动子的可能性。保守序列基序的（近似）起始;（2）基于“模体闭合”的概念，提出了一种高可靠性的模体识别方法。这两个关键的想法是嵌入在一个经典的框架中，通过寻找图中的团基发现，但这个框架实质上更敏感，以及在一个非常嘈杂的背景下的基序发现更有选择性。比较分析表明，与其他六种最先进的预测工具相比，我们的程序在来自一个基因组的大规模启动子数据集上的性能系数从29%提高到41%，并且在另一种跨多个基因组的大规模数据集上也持续大幅提高。通过在大肠杆菌K12的2390个启动子序列上运行BOBRO来识别全局转录调节因子的基序，进一步证明了BOBRO在处理噪声数据方面的能力。
We present a new algorithm, BOBRO, for prediction of cis-regulatory motifs in a given set of promoter sequences. The algorithm substantially improves the prediction accuracy and extends the scope of applicability of the existing programs based on two key new ideas: (i) we developed a highly effective method for reliably assessing the possibility for each position in a given promoter to be the (approximate) start of a conserved sequence motif; and (ii) we developed a highly reliable way for recognition of actual motifs from the accidental ones based on the concept of ‘motif closure’. These two key ideas are embedded in a classical framework for motif finding through finding cliques in a graph but have made this framework substantially more sensitive as well as more selective in motif finding in a very noisy background. A comparative analysis shows that the performance coefficient was improved from 29% to 41% by our program compared to the best among other six state-of-the-art prediction tools on a large-scale data sets of promoters from one genome, and also consistently improved by substantial margins on another kind of large-scale data sets of orthologous promoters across multiple genomes. The power of BOBRO in dealing with noisy data was further demonstrated through identification of the motifs of the global transcriptional regulators by running it over 2390 promoter sequences of Escherichia coli K12.
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影响因子：
4.3
作者：
Siddharthan, Rahul;Siggia, Eric D;van Nimwegen, Erik
通讯作者：
van Nimwegen, Erik
DOI：
10.1142/s0219720003000162
发表时间：
2003-04-01
影响因子：
1
作者：
Olman, Victor;Xu, Dong;Xu, Ying
通讯作者：
Xu, Ying
影响因子：
7.5
作者：
BAILEY, TL;ELKAN, C
通讯作者：
ELKAN, C
准确识别原核基因组中正确长度的顺式调节基序。
影响因子：
14.9
作者：
Li G;Liu B;Xu Y
通讯作者：
Xu Y
影响因子：
14.9
作者：
Neph S;Tompa M
通讯作者：
Tompa M