iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components.
iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components.
复制标题
DOI：
10.3390/ijms15021746
复制
发表时间：
2014-01-24
影响因子：
5.6
通讯作者：
Chou KC
中科院分区：
文献类型：
--
作者：
Qiu WR;Xiao X;Chou KC
减数分裂和重组是DNA系统中共存的两个相反的方面。减数分裂重组作为一种进化的动力，通过产生自然的遗传变异，在卵子和精子的形成中起着非常重要的作用。有趣的是，重组并不是在基因组中随机发生的，而是在称为“热点”的一些基因组区域中具有较高的概率，而在所谓的“冷点”中具有较低的概率。随着后基因组时代基因组序列数据量的不断增加，有效识别热点和冷点的计算方法已成为迫切需要，因为它们可以为我们及时了解减数分裂重组机制和基因组进化过程提供有用的见解。为了满足这一需求，我们开发了一种新的预测器称为"iRSpot-TNCPseAAC"，其中DNA样品通过将其三核苷酸组成（TNC）和根据其遗传密码从DNA样品翻译的蛋白质的伪氨基酸组分（PseAAC）组合来配制。前者用于整合其局部或短程序列顺序信息，而后者用于整合其全局和长程序列顺序信息。与该领域现有的最佳预测器相比，iRSpot-TNCPseAAC在准确率、Mathew相关系数和灵敏度方面都取得了更高的成绩，这表明新的预测器可能成为识别重组热点和冷点的有用工具，或者至少成为现有方法的补充工具。我们注意到，上述将DNA序列顺序信息合并到离散模型中的新方法也可以用于许多其他基因组分析问题。iRSpot-TNCPseAAC的网络服务器可在www.example.com上获得。此外，为了方便绝大多数实验科学家，提供了一个分步指南，说明如何使用当前的Web服务器来获得他们想要的结果，而不需要遵循复杂的数学方程。
Meiosis and recombination are the two opposite aspects that coexist in a DNA system. As a driving force for evolution by generating natural genetic variations, meiotic recombination plays a very important role in the formation of eggs and sperm. Interestingly, the recombination does not occur randomly across a genome, but with higher probability in some genomic regions called “hotspots”, while with lower probability in so-called “coldspots”. With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods for effectively identifying the hotspots and coldspots have become urgent as they can timely provide us with useful insights into the mechanism of meiotic recombination and the process of genome evolution as well. To meet the need, we developed a new predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample according to its genetic codes. The former was used to incorporate its local or short-rage sequence order information; while the latter, its global and long-range one. Compared with the best existing predictor in this area, iRSpot-TNCPseAAC achieved higher rates in accuracy, Mathew’s correlation coefficient, and sensitivity, indicating that the new predictor may become a useful tool for identifying the recombination hotspots and coldspots, or, at least, become a complementary tool to the existing methods. It has not escaped our notice that the aforementioned novel approach to incorporate the DNA sequence order information into a discrete model may also be used for many other genome analysis problems. The web-server for iRSpot-TNCPseAAC is available at http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to obtain their desired result without the need to follow the complicated mathematical equations.
登录
查看更多内容
影响因子：
5.8
作者：
Chou, KC
通讯作者：
Chou, KC
影响因子：
2
作者：
Chen, Yen-Kuang;Li, Kuo-Bin
通讯作者：
Li, Kuo-Bin
DOI：
10.1016/j.bbrc.2006.06.059
发表时间：
2006-08-18
影响因子：
3.1
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
影响因子：
3.4
作者：
Cai, YD;Zhou, GP;Chou, KC
通讯作者：
Chou, KC
DOI：
10.1002/prot.340210406
发表时间：
1995-04-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
CHOU, KC
通讯作者：
CHOU, KC