| KaKs＿Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences |
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| 引用本文： | Zhang Zhang. KaKs＿Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences[J]. 基因组蛋白质组与生物信息学报(英文版), 2022, 20(3): 536-540. DOI: 10.1016/j.gpb.2021.12.002 |
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| 作者姓名： | Zhang Zhang |
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| 基金项目： | the National Natural Science Foundation of China (Grant Nos. 31871328 and 32030021)；;the National Key R&D Program of China (Grant No. 2017YFC0907502)；;the International Partnership Program of the Chinese Academy of Sciences (Grant No. 153F11KYSB20160008)； |
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| 摘 要： | KaKs＿Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs＿Calculator 3.0 shows effectiveness to detect the strength and mode of sele...
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| 收稿时间： | 2021-11-24 |
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences |
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| Zhang Zhang. KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences[J]. Genomics, proteomics & bioinformatics, 2022, 20(3): 536-540. DOI: 10.1016/j.gpb.2021.12.002 |
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| Authors: | Zhang Zhang |
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| Affiliation: | 1. National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;3. China National Center for Bioinformation, Beijing 100101, China;4. University of Chinese Academy of Sciences, Beijing 100049, China |
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| Abstract: | KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001. |
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| Keywords: | KaKs_Calculator Selective pressure Substitution Coding Non-coding |
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