Abstract
PolyAna (available at http://www.biol.sc.edu/~austin/) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous.
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References
Chanock S (2001) Candidate genes and single nucleotide polymorphisms (SNPs) in the study of human disease. Dis Markers 17(2):89–98. Review
Dufour C, Casane D, Denton D, Wickings J, Corvol P, Jeunemaitre X (2000) Human-chimpanzee DNA sequence variation in the four major genes of the renin angiotensin system. Genomics 69(1):14–26
Gray IC, Campbell DA, Spurr NK (2000) Single nucleotide polymorphisms as tools in human genetics Hum Mol Genet 9(16):2403–8. Review
Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4(2):45–61. Review
Hughes AL (2005) Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169(2):533–538
Hughes AL (2007) Micro-scale signature of purifying selection in Marburg virus genomes. Gene 392(1–2):266–272
Hughes AL, Hughes MA (2007) Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol Ecol 16(7):1369–1376
Hughes AL (2009a) Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae. Vaccine 27(11):1685–1690
Hughes AL (2009b) Relaxation of purifying selection on the SAD lineage of live attenuated oral vaccines for rabies virus. Infect Genet Evol 9(5):827–831
Hughes AL (2009c) Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology 393:127–134
Hughes AL, Piontkivska H (2008) Nucleotide sequence polymorphism in circoviruses. Infect Genet Evol 8(2):130–138
Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M (2003) Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc Natl Acad Sci USA 100(26):15754–15757
Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M (2005a) Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding loci. Genetics 170(3):1181–1187
Hughes AL, Packer B, Welch R, Chanock SJ, Yeager M (2005b) High level of functional polymorphism indicates a unique role of natural selection at human immune system loci. Immunogenetics 57(11):821–827
Hughes AL, Hughes MA, Friedman R (2007) Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus. Virus Res 123(2):147–153
Hughes AL, Friedman R, Rivailler P, French JO (2008a) Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol 25(10):2199–2209
Hughes AL, Welch R, Puri V, Matthews C, Haque K, Chanock SJ, Yeager M (2008b) Genome-wide SNP typing reveals signatures of population history. Genomics 92(1):1–8
Irausquin SJ, Hughes AL (2008) Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures. J Gen Virol 89(Pt 8):1921–1929
Irausquin SJ, Hughes AL (2010) Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.Virus Res 147(2):202–7
Kearney M, Palmer S, Maldarelli F, Shao W, Polis MA, Mican J, Rock-Kress D, Margolick JB, Coffin JM, Mellors JW (2008) Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase. AIDS 22(4):497–501
Landegren U, Nilsson M, Kwok PY (1998) Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res 8(8):769–76. Review
Li WH, Sadler LA (1991) Low genetic diversity in man. Genetics 129(2):513–523
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452
Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R (2004) Parallel genotyping of over 10, 000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 14(3):414–425
Morin PA, Luikart G, Wayne RK et al (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19(4):208–216. Review
Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York
Putaporntip C, Udomsangpetch R, Pattanawong U, Cui L, Jongwutiwes S (2010) Genetic diversity of the Plasmodium vivax merozoite surface protein-5 locus from diverse geographic origins. Gene 456(1–2):24–35
Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–333. Review
Rozen S, Marszalek JD, Alagappan RK, Skaletsky H, Page DC (2009) Remarkably little variation in proteins encoded by the Y chromosome’s single-copy genes, implying effective purifying selection. Am J Hum Genet 85(6):923–928
Seddon JM, Parker HG, Ostrander EA, Ellegren H (2005) SNPs in ecological and conservation studies: a test in the Scandinavian wolf population. Mol Ecol 14(2):503–511
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–9
Acknowledgments
This work was supported by the National Institutes of Health [GM43940 to A.L.H].
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Knapp, E.W., Irausquin, S.J., Friedman, R. et al. PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. Conservation Genet Resour 3, 429–431 (2011). https://doi.org/10.1007/s12686-010-9372-5
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DOI: https://doi.org/10.1007/s12686-010-9372-5