iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition.
iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition.
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iRSpot-PseDNC：识别具有伪二核苷酸组成的重组点
DOI：
10.1093/nar/gks1450
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发表时间：
2013-04-01
影响因子：
14.9
通讯作者：
Chou KC
中科院分区：
文献类型：
--
作者：
Chen W;Feng PM;Lin H;Chou KC
减数分裂重组是一个重要的生物学过程。作为进化的主要驱动力，重组提供了自然的新的遗传变异组合。减数分裂重组不是在整个基因组中随机发生，而是在一些频率较高的基因组区域(所谓的“热点”)和频率较低的其他区域(所谓的“冷点”)发生。因此，这些热点和冷点的信息将为深入研究重组机制和基因组进化过程提供有用的见解。到目前为止，重组区域的确定主要是通过实验来确定的，这既昂贵又耗时。随着后基因组时代产生的基因组序列的雪崩，人们迫切希望开发出快速有效地识别重组区域的自动化方法。在这项研究中，开发了一种称为iRSpot-PseDNC的预测因子，用于识别重组热点和冷点。在新的预测器中，DNA序列样本由一个新的特征向量组成，即所谓的伪二核苷酸组成(PseDNC)，其中包含了DNA的六个局部结构属性，即三个角度参数(扭转、倾斜和滚动)和三个平移参数(移动、滑动和上升)。通过严格的折刀检验，iRSpot-PseDNC在确定酿酒酵母重组点上的总体成功率为82%，这表明新的预测器是有前途的，或者至少可以成为这一领域现有方法的补充工具。虽然用于训练和测试当前方法的基准数据集来自酿酒酵母，但基本方法也可以扩展到处理所有其他基因组。特别是，我们没有注意到，PseDNC方法也可以用于研究许多其他与DNA相关的问题。作为一个用户友好的Web服务器，iRSpot-PseDNC可以在http://lin.uestc.edu.cn/server/iRSpot-PseDNC.上免费访问
Meiotic recombination is an important biological process. As a main driving force of evolution, recombination provides natural new combinations of genetic variations. Rather than randomly occurring across a genome, meiotic recombination takes place in some genomic regions (the so-called ‘hotspots’) with higher frequencies, and in the other regions (the so-called ‘coldspots’) with lower frequencies. Therefore, the information of the hotspots and coldspots would provide useful insights for in-depth studying of the mechanism of recombination and the genome evolution process as well. So far, the recombination regions have been mainly determined by experiments, which are both expensive and time-consuming. 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 recombination regions. In this study, a predictor, called ‘iRSpot-PseDNC’, was developed for identifying the recombination hotspots and coldspots. In the new predictor, the samples of DNA sequences are formulated by a novel feature vector, the so-called ‘pseudo dinucleotide composition’ (PseDNC), into which six local DNA structural properties, i.e. three angular parameters (twist, tilt and roll) and three translational parameters (shift, slide and rise), are incorporated. It was observed by the rigorous jackknife test that the overall success rate achieved by iRSpot-PseDNC was >82% in identifying recombination spots in Saccharomyces cerevisiae, indicating the new predictor is promising or at least may become a complementary tool to the existing methods in this area. Although the benchmark data set used to train and test the current method was from S. cerevisiae, the basic approaches can also be extended to deal with all the other genomes. Particularly, it has not escaped our notice that the PseDNC approach can be also used to study many other DNA-related problems. As a user-friendly web-server, iRSpot-PseDNC is freely accessible at http://lin.uestc.edu.cn/server/iRSpot-PseDNC.
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影响因子：
3.7
作者：
Chou KC;Wu ZC;Xiao X
通讯作者：
Xiao X
影响因子：
5.8
作者：
Chou, KC
通讯作者：
Chou, KC
影响因子：
3
作者：
Chou, KC
通讯作者：
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影响因子：
2.9
作者：
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通讯作者：
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通过计算 DNA 结构特性预测复制起点
影响因子：
3.5
作者：
Chen, Wei;Feng, Pengmian;Lin, Hao
通讯作者：
Lin, Hao