title: Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships.
abstract: Amino acid substitution tables are essential for the proper alignment of protein sequences, and alignment scores based on them can be transformed into distance measures by various means. In the simplest case, the negative log of the score is used. This Poisson relationship assumes that all sites are equally likely to change, however. A more accurate relationship would correct for different rates of change at each residue position. Recently, Grishin (J. Mol. Evol. 41:675-679, 1995) published a set of simple equations that correct for various circumstances, including different rates of change at different sites. We have used these equations in conjunction with similarity scores that take into account constraints on amino acid interchange. Simulation studies show a linear relationship between these calculated distances and the numbers of allowed mutations based on the observed variation of rate at all sites in various proteins.
authors.affiliation: Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0634, USA.
authors.forename: D F
authors.initials: DF
authors.lastname: Feng
authors.forename: R F
authors.initials: RF
authors.lastname: Doolittle
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D003198:Computer Simulation; D004081:Dihydroorotate Oxidase / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000737:chemistry; D009154:Mutation; D010735:Phosphoglycerate Kinase / Q000737:chemistry; D010802:Phylogeny; D016012:Poisson Distribution; D011336:Probability; D016415:Sequence Alignment; D013045:Species Specificity; D013482:Superoxide Dismutase / Q000737:chemistry; D013995:Time; D014305:Triose-Phosphate Isomerase / Q000737:chemistry
chemical_list: D004798:Enzymes; D013482:Superoxide Dismutase; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases; D004081:Dihydroorotate Oxidase; D010735:Phosphoglycerate Kinase; D014305:Triose-Phosphate Isomerase