Investigating selection on viruses: A statistical alignment approach

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  De Groot, Saskia ^a   Mailund, Thomas ^a,b   Lunter, Gerton ^a   Hein, Jotun ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY DISTANCE; HIGH MUTATION RATE; NEGATIVE SELECTION; PARAMETRIC INFERENCE; SELECTION PARAMETERS; SIMULATION STUDIES; STANDARD PRACTICES; STATISTICAL ALIGNMENTS;

ESTIMATION; GENES; UNCERTAINTY ANALYSIS; VIRUSES;

ALIGNMENT;

ACCURACY; ARTICLE; CONTROLLED STUDY; GENETIC CODE; GENETIC CONSERVATION; GENETIC DISTANCE; GENETIC SELECTION; GENETIC VARIABILITY; HEPATITIS B VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 2; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PROCESS MODEL; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL PARAMETERS; VIRAL GENETICS; BIOMETRY; CHROMOSOME MAP; DNA SEQUENCE; GENETICS; HEPATITIS B; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PREDICTION AND FORECASTING; UNCERTAINTY; VIRUS; VIRUS GENOME;

BIOMETRY; CHROMOSOME MAPPING; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENOME, VIRAL; HEPATITIS B; HIV-2; PHYLOGENY; PREDICTIVE VALUE OF TESTS; READING FRAMES; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; UNCERTAINTY; VIRUSES;

EID: 47949130368     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-304     Document Type: Article

References (26)

1. De Groot S Mailund T Hein J Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure Bioinformatics 2007, 23(9):1080-1089 17341494
2. de Oliveira T Salemi M Gordon M Vandamme A-M van Rensburg EJ Engelbrecht S Coovadia HM Cassol S Mapping Sites of Positive Selection and Amino Acid Diversification in the HIV Genome Genetics 2004, 167:1047-1058 1470929 15280222
3. Durbin R Eddy S Krogh A Mitchison G Biological Sequence Analysis Cambridge University Press 1998
4. Guyader S Ducray DG Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products Journal of General Virology 2002, 83:1799-1807 12075102
5. Hein J Støvlbæk J A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frame Journal of Molecular Evolution 1995, 40(2):181-189 7699722
6. Hein J Støvlbæk J Combined DNA and Protein Alignment Methods in Enzymology 1996, 266:402-418 8743696
7. Hughes AL Hughes MAK Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes Virus Research 2005, 113:81-88 15913825
8. Kimura M A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences Journal of Molecular Evolution 1980, 16:111-120 7463489
9. Lunter GA Drummond AJ Miklós I Hein J Statistical Alignment: Recent Progress, New Applications, and Challenges: Statistical methods in Molecular Evolution Springer Verlag's Series in Statistics in Health and Medicine 2004.
10. Lunter GA Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes Bioinformatics 2007, 23(13):i289-i296 17646308
11. Lunter GA HMMoC - a compiler for hidden Markov models Bioinformatics 2007, 23(18):2485-2487 17623703
12. Metzler D Fleissner R Wakolbinger A von Haeseler A Assessing Variability by Joint Sampling of Alignments and Mutation Rates Journal of Molecular Evolution 2001, 53(1):660-669 11677626
13. McCauley S de Groot S Mailund T Hein J Annotation of Selection Strengths in Viral Genomes Bioinformatics 2007. Advance Access 17921171
14. Mizokami M Orito E Ohba K Ikeo K Lau JY Gojobori T Constrained evolution with respect to gene overlap of Hepatitis B Virus J Mol Evol 1997, 44(Suppl 1):S83-90 9071016
15. Osiowy C Giles E Tanaka Y Mizokami M Minuk GY Molecular Evolution of Hepatitis B Virus over 25 Years Journal of Virology 2006, 80(21):10307-10314 1641782 17041211
16. Pavesi A Origin and evolution of overlapping genes in the family Microviridae, Journal of General Virology 2006, 87:1013-1017
17. Pedersen AM Jensen JL A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames Mol Biol Evol 2001, 18(5):763-776 11319261
18. Rogozin I Spiridinov AN Sorokin AV Wolf YI Jordan IK Tatusov RL Koonin EV Purifying and directional selection in overlapping prokaryotic genes Trends in Genetics 2002, 18(5):228-232 12047938
19. Spiropoulou CF Nichol ST A small highly basic protein is encoded in overlapping reading frame within the P gene of vesicular stomatitis virus Journal of Virology 1993, 67:3103-3110 237647 8388490
20. Thompson JD Higgins DG Gibson TJ ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 1994, 22(22):4673-4680 308517 7984417
21. Thorne JL Kishino H Felsenstein J An evolutionary model for maximum likelihood alignment of DNA sequences Journal of Molecular Evolution 1991, 33:114-124 1920447
22. Walewski JL Keller TR Stump DD Branch AD Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame RNA 2001, 7(5):710-721 1370123 11350035
23. Zuker M Suboptimal sequence alignment in molecular biology. Alignment with error analysis Journal of Molecular Biology 1991, 221:403-420 1920426
24. Zhang J The infancy of duplicate genes Heredity 2004, 92:479-480
25. All data used is publicly released on the GenBank database http://www.ncbi.nlm.nih.gov/
26. ClustalW Software http://www.ebi.ac.uk/clustalw/