A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationship: An application to papillomavirus DNA sequences

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Qiao, Baozhen ^a   Weigel, Ronald M ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLETE GENOMES; GENBANK DATABASE; GENETIC RELATEDNESS; GENETIC RELATIONSHIPS; GENETIC SIMILARITIES; GENOTYPING METHODS; LABORATORY ERRORS; PARTIAL GENOMES;

BIOLOGY; COMPUTER SIMULATION; GENES;

DNA SEQUENCES;

DNA FRAGMENT; GENOMIC DNA; VIRUS DNA;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; GENBANK; GENETIC ANALYSIS; GENETIC CORRELATION; GENETIC DATABASE; GENETIC SELECTION; GENETIC SIMILARITY; GENOTYPE; INTERMETHOD COMPARISON; MOLECULAR PHYLOGENY; MOLECULAR SIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PARTITION COEFFICIENT; RESTRICTION FRAGMENT; STANDARDIZATION; VIRAL GENETICS; VIRUS ISOLATION; ANIMAL; BOVINE PAPILLOMAVIRUS TYPE 1; COMPARATIVE STUDY; DOG; GENETICS; HUMAN; PAN TROGLODYTES; PHYLOGENY; PROCEDURES; RESTRICTION MAPPING; SPECIES DIFFERENCE; VIROLOGY; VIRUS GENOME;

PAPILLOMAVIRUS;

ANIMALS; BOVINE PAPILLOMAVIRUS 1; COMPUTER SIMULATION; DATABASES, GENETIC; DNA, VIRAL; DOGS; GENOME, VIRAL; GENOTYPE; HUMANS; PAN TROGLODYTES; PAPILLOMAVIRIDAE; PHYLOGENY; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 13244275011     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-102     Document Type: Article

References (42)

1. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B: Interpreting chromosomal DNA restriction patterns produced by pulse-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995, 33: 233-2239.
2. Salamon H, Behr MA, Rhee JT, Small PM: Genetic distances for the study of infectious disease epidemiology. Am J Epidemiol 2000, 151:324-334.
3. Upholt WB: Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. Nucleic Acids Res 1977, 4:1257-1265.
4. Dowling TE, Moritz C, Palmer JD, Riesenberg LH: Nucleic acids III: analysis of fragments and restriction sites. In Molecular Systematics Edited by: Hillis DM, Moritz C, Mable BK. Sunderland, Massachusetts: Sinauer; 1996:249-320.
5. Lynch M: The similarity index and DNA fingerprinting. Mol Biol Evol 1990, 7:478-484.
6. Call DR, Hallett JG, Mech SG, Evans M: Considerations for measuring genetic variation and population structure with multilocus fingerprinting. Mol Ecol 1998, 7:1337-1346.
7. Römling U, Grothues D, Heuer T, Tümmler B: Physical genome analysis of bacteria. Electrophoresis 1992, 13 626-631.
8. Holt RJ, Strike P, Bruce DK: Phylogenetic analysis of tnpR genes in mercury resistant soil bacteria: the relationship between DNA sequencing and RFLP typing approaches. FEMS Microbiol Lett 1996, 144:95-102.
9. Arens M: Methods for subtyping and molecular comparison of human viral genomes. Clin Microbiol Rev 1999, 12:612-626.
10. Takewaki S, Okuzumi K, Manabe I, Tanimura M, Miyamura K, Nakahara K, Yazaki Y, Ohkubo A, Nagai R: Nucleotide sequence comparison of the mycobacterial dnaJ gene and PCR-restriction fragment length polymorphism analysis for identification of mycobacterial species. Int J Syst Bacteriol 1994, 44:159-166.
11. Russo CAM, Takezaki N, Nei M: Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol 1996, 13:525-536.
12. Olive DM, Bean P: Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 1999, 37:1661-1669.
13. Goldberg TL, Weigel RM, Hahn EC, Scherba G: Comparative utility of restriction fragment length polymorphism analysis and gene sequencing to the molecular epidemiological investigation of a viral outbreak. Epidemiol Infect 2001, 126:415-424.
14. Nei M, Kumar S: Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000.
15. Qiao B: Investigation of the accuracy of partial genome sequencing and restriction fragment analysis in determination of genetic relationships: a computer simulation study. Ph.D dissertation, University of Illinois at Urbana-Champaign 2003.
16. Chan S-Y, Bernard H-U, Ratterree M, Birkebak TA, Faras AJ, Ostrow RS: Genomic diversity and evolution of papillomaviruses in rhesus monkeys. J Virol 1997, 71:4938-4943.
17. De Villiers E-M, Fauquet C, Broker TR, Bernard H-U, zur Hausen H: Classification of papillomaviruses. Virology 2004, 324:17-27.
18. Gao F, Yue L, Robertson DL, Hill SC, Hui H, Biggar RJ, Neequaye AE, Whelan TM, Ho DD, Shaw GM, Sharp PM, Hahn BH: Genetic diversity of human immunodeficiency virus type 2: evidence of distinct sequence subtypes with differences in virus biology. J Virol 1994, 68:7433-7447.
19. Greiser-Wilke I, Fritzmeier J, Koenen F, Vanderhallen H, Rutili D, de Mia G-M, Romero L, Rosell R, Sanchez-Vizcaino JM, San Gabriel A: Molecular epidemiology of a large classical swine fever epidemic in the European Union in 1997-1998. Vet Microbiol 2000, 77:17-27.
20. Forsberg R, Oleksiewicz MB, Krabbe Petersen A-M, Hein J, Bøtner A, Storgaard T: A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease. Virology 2001, 289:174-179.
21. Knowles NJ, Samuel AR: Molecular epidemiology of foot-and-mouth disease virus. Virus Res 2003, 91:65-80.
22. Goering RV, Duensing TD: Rapid field inversion gel electrophoresis in combination with a rRNA gene probe in the epidemiological evaluation of Staphylococci. J Clin Microbiol 1990, 28:426-429.
23. Maslow JN, Mulligan ME, Arbeit RD: Molecular epidemiology: application of contemporary techniques to the typing of microorganisms. Clin Infect Dis 1993, 17:153-164.
24. Tenover FC, Arbeit RD, Goering RV, the Molecular Typing Working Group of the Society for Healthcare Epidemiology of America: How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Infect Control 1997, 18:426-439.
25. Laber TL, Iverson JT, Liberty JA, Giese SA: The evaluation and implementation of match criteria for forensic analysis of DNA. J Forensic Sci 1995, 40:1058-1064.
26. Duewer DL, Lalonde SA, Aubin RA, Fourney RM, Reeder DJ: Interlaboratory comparison of autoradiographic DNA profiling measurements: precision and concordance. J Forensic Sci 1998, 43:465-471.
27. Gill P, Evett IW, Woodroffe S, Lygo JE, Millican E, Webster M: Databases, quality control and interpretation of DNA profiling in the Home Office Forensic Science Service. Electrophoresis 1991, 12:204-209.
28. Hillis DM, Mable BK, Larson A, Davis SK, Zimmer EA: Nucleic acids IV: sequencing and cloning. In Molecular Systematics Edited by: Hillis DM, Moritz C, Mable BK. Sunderland, Massachusetts: Sinauer; 1996:321-381.
29. Genbank Database [http://www.ncbi.nlm.nih.gov/Genbank]
30. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
31. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120.
32. Kimura M: Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 1981, 78:454-458.
33. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning - A Laboratory Manual 2nd edition. New York: Cold Spring Harbor Laboratory Press; 1989.
34. Nakisa RC: DIGEST, version 1.0. London: Imperial College of Science, Technology and Medicine 1993 [http://iubio.bio.indiana.edu/soft/molbio/ibmpc].
35. Nei M: Molecular Evolutionary Genetics New York: Columbia University Press; 1987.
36. Mantel N: The detection of disease clustering and a generalized regression approach. Cancer Res 1967, 27: 09-220.
37. Saitou N, Nei M: The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4: 06-425.
38. Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA: Molecular Evolutionary Genetics Analysis Software, version 2.1. Tempe: Arizona State University 2001 [http://www.megasoftware.net].
39. Swafford DL, Olsen GJ, Waddell, Hillis DM: Phylogenetic Inference. In Molecular Systematics Edited by: Hillis DM, Moritz C, Mable BK. Sunderland, Massachusetts: Sinauer; 1996:407-514.
40. Page RDM: COMPONENT, version 2.0. London: The Natural History Museum 1993 [http://taxonomy.zoology.gla.ac.uk/rod/cpw.html].
41. Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosci 1981, 53:131-147.
42. Penny D, Hendy MD: The use of tree comparison metrics. Syst Zool 1985, 34:75-82.