Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships
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...
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| Veröffentlicht in: | Journal of molecular evolution 1997-04, Vol.44 (4), p.361-370 |
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| container_title | Journal of molecular evolution |
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| creator | Feng, D F Doolittle, R F |
| description | 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. |
| doi_str_mv | 10.1007/PL00006155 |
| format | Article |
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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.</description><identifier>ISSN: 0022-2844</identifier><identifier>EISSN: 1432-1432</identifier><identifier>DOI: 10.1007/PL00006155</identifier><identifier>PMID: 9089075</identifier><language>eng</language><publisher>Germany: Springer Nature B.V</publisher><subject>Amino Acid Sequence ; Amino acids ; Animals ; Biological Evolution ; Computer Simulation ; Dihydroorotate Oxidase - chemistry ; Enzymes - chemistry ; Enzymes - genetics ; Evolution ; Glyceraldehyde-3-Phosphate Dehydrogenases - chemistry ; Molecular biology ; Mutation ; Phosphoglycerate Kinase - chemistry ; Phylogeny ; Poisson Distribution ; Probability ; Proteins ; Sequence Alignment ; Simulation ; Species Specificity ; Superoxide Dismutase - chemistry ; Time ; Triose-Phosphate Isomerase - chemistry</subject><ispartof>Journal of molecular evolution, 1997-04, Vol.44 (4), p.361-370</ispartof><rights>Springer-Verlag New York Inc. 1997</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c341t-f442bdbfb1581655b626627f0a4b30bc72ca227bde9428d234720b9bfb0c19453</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9089075$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Feng, D F</creatorcontrib><creatorcontrib>Doolittle, R F</creatorcontrib><title>Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships</title><title>Journal of molecular evolution</title><addtitle>J Mol Evol</addtitle><description>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.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Animals</subject><subject>Biological Evolution</subject><subject>Computer Simulation</subject><subject>Dihydroorotate Oxidase - chemistry</subject><subject>Enzymes - chemistry</subject><subject>Enzymes - genetics</subject><subject>Evolution</subject><subject>Glyceraldehyde-3-Phosphate Dehydrogenases - chemistry</subject><subject>Molecular biology</subject><subject>Mutation</subject><subject>Phosphoglycerate Kinase - chemistry</subject><subject>Phylogeny</subject><subject>Poisson Distribution</subject><subject>Probability</subject><subject>Proteins</subject><subject>Sequence Alignment</subject><subject>Simulation</subject><subject>Species Specificity</subject><subject>Superoxide Dismutase - chemistry</subject><subject>Time</subject><subject>Triose-Phosphate Isomerase - 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chemistry</topic><topic>Enzymes - chemistry</topic><topic>Enzymes - genetics</topic><topic>Evolution</topic><topic>Glyceraldehyde-3-Phosphate Dehydrogenases - chemistry</topic><topic>Molecular biology</topic><topic>Mutation</topic><topic>Phosphoglycerate Kinase - chemistry</topic><topic>Phylogeny</topic><topic>Poisson Distribution</topic><topic>Probability</topic><topic>Proteins</topic><topic>Sequence Alignment</topic><topic>Simulation</topic><topic>Species Specificity</topic><topic>Superoxide Dismutase - chemistry</topic><topic>Time</topic><topic>Triose-Phosphate Isomerase - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Feng, D F</creatorcontrib><creatorcontrib>Doolittle, R F</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - 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| subjects | Amino Acid Sequence Amino acids Animals Biological Evolution Computer Simulation Dihydroorotate Oxidase - chemistry Enzymes - chemistry Enzymes - genetics Evolution Glyceraldehyde-3-Phosphate Dehydrogenases - chemistry Molecular biology Mutation Phosphoglycerate Kinase - chemistry Phylogeny Poisson Distribution Probability Proteins Sequence Alignment Simulation Species Specificity Superoxide Dismutase - chemistry Time Triose-Phosphate Isomerase - chemistry |
| title | Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships |
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