OpenLB
Open Library of Bioscience
Advanced Search
Genomics, proteomics & bioinformatics
06, 2022;20 (3): 536-540.

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

Zhang Zhang
Author Information
  1. 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. Electronic address: zhangzhang@big.ac.cn.
PMID: 34990803 DOI: 10.1016/j.gpb.2021.12.002

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.

Keywords

Coding KaKs_Calculator Non-coding Selective pressure Substitution

References

  1. Mol Biol Evol. 1994 Sep;11(5):725-36 [PMID: 7968486]
  2. Mol Biol Evol. 1993 Mar;10(2):271-81 [PMID: 8487630]
  3. Mol Biol Evol. 2013 Apr;30(4):772-80 [PMID: 23329690]
  4. BMC Evol Biol. 2008 Jan 23;8:17 [PMID: 18215302]
  5. Science. 2004 May 28;304(5675):1321-5 [PMID: 15131266]
  6. Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81 [PMID: 17127215]
  7. Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81 [PMID: 22390928]
  8. Brief Bioinform. 2019 Sep 27;20(5):1853-1864 [PMID: 30010717]
  9. Trends Genet. 2014 Apr;30(4):121-3 [PMID: 24613441]
  10. Nucleic Acids Res. 2013 Sep;41(17):8220-36 [PMID: 23847102]
  11. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028 [PMID: 33270901]
  12. RNA Biol. 2017 Dec 2;14(12):1705-1714 [PMID: 28837398]
  13. Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80 [PMID: 20451164]
  14. Annu Rev Genet. 2008;42:287-99 [PMID: 18983258]
  15. J Mol Evol. 1985;22(2):160-74 [PMID: 3934395]
  16. Br J Cancer. 2016 Jun 14;114(12):1395-404 [PMID: 27172249]
  17. Nucleic Acids Res. 2022 Jan 7;50(D1):D190-D195 [PMID: 34751395]
  18. J Mol Evol. 2009 Apr;68(4):414-23 [PMID: 19308632]
  19. Mol Biol Evol. 2000 Jan;17(1):32-43 [PMID: 10666704]
  20. Nucleic Acids Res. 2022 Jan 7;50(D1):D27-D38 [PMID: 34718731]
  21. Nucleic Acids Res. 2019 Jan 8;47(D1):D128-D134 [PMID: 30329098]
  22. Trends Genet. 2002 Sep;18(9):486 [PMID: 12175810]
  23. Genomics Proteomics Bioinformatics. 2021 Jun;19(3):377-393 [PMID: 34284134]
  24. Methods Mol Biol. 2012;856:141-59 [PMID: 22399458]
  25. Mol Biol Evol. 1985 Mar;2(2):150-74 [PMID: 3916709]
  26. BMC Evol Biol. 2011 Apr 16;11:102 [PMID: 21496275]
  27. Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
  28. J Mol Evol. 1993 Jan;36(1):96-9 [PMID: 8433381]
  29. Mol Biol Evol. 2010 Jun;27(6):1226-34 [PMID: 20150340]
  30. Nat Rev Cancer. 2018 Jan;18(1):5-18 [PMID: 29170536]
  31. Genetics. 2004 Jun;167(2):949-58 [PMID: 15238543]
  32. Cell Physiol Biochem. 2018;47(3):893-913 [PMID: 29843138]
  33. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):602-610 [PMID: 34536568]
  34. Genomics Proteomics Bioinformatics. 2006 Nov;4(4):259-63 [PMID: 17531802]
  35. Nature. 2012 Sep 6;489(7414):57-74 [PMID: 22955616]
  36. J Mol Med (Berl). 2013 Jul;91(7):791-801 [PMID: 23529762]
  37. Mol Biol Evol. 1986 Sep;3(5):418-26 [PMID: 3444411]
  38. Nucleic Acids Res. 2013 Feb 1;41(4):2073-94 [PMID: 23293005]
  39. Mol Biol Evol. 2004 Dec;21(12):2290-8 [PMID: 15329386]
  40. Nucleic Acids Res. 2000 Mar 1;28(5):1221-7 [PMID: 10666466]
  41. Trends Genet. 1999 Apr;15(4):134-5 [PMID: 10203817]
  42. Nature. 2009 Mar 12;458(7235):223-7 [PMID: 19182780]
  43. OMICS. 2019 Nov;23(11):549-559 [PMID: 31689173]
  44. Nat Rev Genet. 2011 Jan;12(1):32-42 [PMID: 21102527]
  45. Biochem Soc Trans. 2020 Aug 28;48(4):1545-1556 [PMID: 32756901]
  46. BMC Evol Biol. 2006 Jun 02;6:44 [PMID: 16740169]
  47. Mol Biol Evol. 2007 Feb;24(2):522-31 [PMID: 17122369]

MeSH Term

Selection, Genetic
Genome
Evolution, Molecular
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

BioCode: BT000001 (KaKs_Calculator)

Word Cloud

Created with Highcharts 10.0.0sequencesKaKs_Calculator30codingnon-codingsubstitutionrateselectionpressureratioSelectiveCodingNon-codingupdatedtoolkitcapablecalculatingselectiveSimilarnonsynonymous/synonymouscanquantifiednucleotidesynonymousadjacenttestifiedempiricaldatashowseffectivenessdetectstrengthmodeoperatedmolecularaccordinglydemonstratinggreatpotentialachievegenome-widescannaturaldiverseidentificationpotentiallyfunctionalelementswhole-genomescalepackagefreelyavailableacademicusehttps://ngdccncbaccn/biocode/tools/BT0000010:CalculatingPressureSequencesSubstitution

Similar Articles

Cited By