Comparative Study
doi: 10.1093/oxfordjournals.molbev.a040153.
A codon-based model of nucleotide substitution for protein-coding DNA sequences
Affiliations
- PMID: 7968486
- DOI: 10.1093/oxfordjournals.molbev.a040153
Item in Clipboard
Comparative Study
A codon-based model of nucleotide substitution for protein-coding DNA sequences
Mol Biol Evol.
1994 Sep.
Abstract
A codon-based model for the evolution of protein-coding DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.
Similar articles
-
Codon substitution models based on residue similarity and their applications.Gene. 2012 Nov 1;509(1):136-41. doi: 10.1016/j.gene.2012.07.075. Epub 2012 Aug 10. Gene. 2012. PMID: 22902303
-
Relating physicochemical properties of amino acids to variable nucleotide substitution patterns among sites.Pac Symp Biocomput. 2000:81-92. Pac Symp Biocomput. 2000. PMID: 10902158
-
Models of amino acid substitution and applications to mitochondrial protein evolution.Mol Biol Evol. 1998 Dec;15(12):1600-11. doi: 10.1093/oxfordjournals.molbev.a025888. Mol Biol Evol. 1998. PMID: 9866196
-
Phase-dependent nucleotide substitution in protein-coding sequences.Biochem Biophys Res Commun. 2007 Apr 13;355(3):599-602. doi: 10.1016/j.bbrc.2007.01.006. Epub 2007 Jan 10. Biochem Biophys Res Commun. 2007. PMID: 17300744 Review.
-
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.Mol Biol Evol. 1985 Mar;2(2):150-74. doi: 10.1093/oxfordjournals.molbev.a040343. Mol Biol Evol. 1985. PMID: 3916709 Review.
Cited by
-
Genetic evolution of the neuraminidase of influenza A (H3N2) viruses from 1968 to 2009 and its correspondence to haemagglutinin evolution.J Gen Virol. 2012 Sep;93(Pt 9):1996-2007. doi: 10.1099/vir.0.043059-0. Epub 2012 Jun 20. J Gen Virol. 2012. PMID: 22718569 Free PMC article.
-
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.Genome Biol Evol. 2015 Mar 5;7(4):1002-15. doi: 10.1093/gbe/evv044. Genome Biol Evol. 2015. PMID: 25747252 Free PMC article.
-
Distinctive patterns of evolution of the δ-globin gene (HBD) in primates.PLoS One. 2015 Apr 8;10(4):e0123365. doi: 10.1371/journal.pone.0123365. eCollection 2015. PLoS One. 2015. PMID: 25853817 Free PMC article.
-
Hepatitis C virus adaptation to T-cell immune pressure.ScientificWorldJournal. 2013;2013:673240. doi: 10.1155/2013/673240. Epub 2013 Mar 11. ScientificWorldJournal. 2013. PMID: 23554569 Free PMC article. Review.
-
Differential evolution and neofunctionalization of snake venom metalloprotease domains.Mol Cell Proteomics. 2013 Mar;12(3):651-63. doi: 10.1074/mcp.M112.023135. Epub 2012 Dec 12. Mol Cell Proteomics. 2013. PMID: 23242553 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical
