期刊
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
卷 14, 期 8, 页码 883-891出版社
IVYSPRING INT PUBL
DOI: 10.7150/ijbs.24616
关键词
Recombination spot; 5-step rules; Key hexamers; PseKNC; SVM; Webserver
资金
- National Nature Scientific Foundation of China [61772119, 31771471]
- Applied Basic Research Program of Sichuan Province [2015JY0100]
- Fundamental Research Funds for the Central Universities of China [ZYGX2015Z006, ZYGX2016J125, ZYGX2016J118]
- Natural Science Foundation for Distinguished Young Scholar of Hebei Province [C2017209244]
- Program for the Top Young Innovative Talents of Higher Learning Institutions of Hebei Province [BJ2014028]
Meiotic recombination caused by meiotic double-strand DNA breaks. In some regions the frequency of DNA recombination is relatively higher, while in other regions the frequency is lower: the former is usually called recombination hotspot, while the latter the recombination coldspot. Information of the hot and cold spots may provide important clues for understanding the mechanism of genome revolution. Therefore, it is important to accurately predict these spots. In this study, we rebuilt the benchmark dataset by unifying its samples with a same length (131 bp). Based on such a foundation and using SVM (Support Vector Machine) classifier, a new predictor called iRSpot-Pse6NC was developed by incorporating the key hexamer features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. It has been observed via rigorous cross-validations that the proposed predictor is superior to its counterparts in overall accuracy, stability, sensitivity and specificity. For the convenience of most experimental scientists, the web-server for iRSpot-Pse6NC has been established at http://lin-group.cn/server/iRSpot-Pse6NC, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.
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