Zhang Zhang
National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Genomics Proteomics Bioinformatics. 2022 Jun;20(3):536-540. doi: 10.1016/j.gpb.2021.12.002. Epub 2022 Jan 3.
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.
KaKs_Calculator 3.0是一个经过更新的工具包，能够计算编码序列和非编码序列上的选择压力。与编码序列的非同义/同义替换率比值类似，非编码序列上的选择可以量化为非编码核苷酸替换率与相邻编码序列同义替换率的比值。经实证数据验证，KaKs_Calculator 3.0在检测分子序列上的选择强度和模式方面表现出有效性，从而证明了其在全基因组范围内扫描不同序列上的自然选择以及在全基因组规模上鉴定潜在功能元件的巨大潜力。KaKs_Calculator 3.0软件包仅可供学术使用，可从https://ngdc.cncb.ac.cn/biocode/tools/BT000001免费获取。
