iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.
iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.
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iPro54-PseKNC：基于序列的预测因子，用于识别具有伪 k 元核苷酸组成的原核生物中的 sigma-54 启动子
DOI：
10.1093/nar/gku1019
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发表时间：
2014-12-01
影响因子：
14.9
通讯作者：
Chou KC
中科院分区：
文献类型：
--
作者：
Lin H;Deng EZ;Ding H;Chen W;Chou KC
σ54启动子在原核基因组中是独特的，负责转录碳和氮相关基因。随着后基因组时代产生的基因组序列的大量涌现，非常需要开发自动化方法来快速有效地识别 σ54 启动子。这里开发了一种名为“iPro54-PseKNC”的预测器。在预测器中，DNA 序列样本由一种称为“伪 k 元组核苷酸组成”的新型特征向量构成，并通过增量特征选择程序进一步优化。 iPro54-PseKNC 的性能通过严格的基准数据集上的严格折刀交叉验证测试进行了检查。作为一个用户友好的网络服务器，iPro54-PseKNC 可以通过 http://lin.uestc.edu.cn/server/iPro54-PseKNC 免费访问。为了方便绝大多数实验科学家，提供了有关如何使用网络服务器获得所需结果的分步协议指南，而无需遵循本文中仅为其完整性而提出的复杂数学。同时，我们还通过深入的统计分析发现，转录起始位点和翻译起始位点之间的距离分布受gamma分布的支配，这可能为研究σ54启动子提供基本的物理原理。
The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters.
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影响因子：
5.8
作者：
Chou, KC
通讯作者：
Chou, KC
影响因子：
2
作者：
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通讯作者：
Li, Kuo-Bin
影响因子：
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作者：
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通讯作者：
de Lorenzo, V
影响因子：
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iRSpot-PseDNC：识别具有伪二核苷酸组成的重组点
影响因子：
14.9
作者：
Chen W;Feng PM;Lin H;Chou KC
通讯作者：
Chou KC