KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences

Zhang Zhang ^{1, 2, 3, 4}

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 |

National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China |

⁴

University of Chinese Academy of sciences, Beijing 100049, China |

Publication type: Journal Article

Publication date: 2022-06-01

Elsevier

Journal: Genomics, Proteomics and Bioinformatics

SJR: —

CiteScore: —

Impact factor: —

ISSN: 16720229

DOI: 10.1016/j.gpb.2021.12.002

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Biochemistry

Molecular Biology

Genetics

Computational Mathematics

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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