메뉴 건너뛰기




Volumn 15, Issue 7, 2008, Pages 881-898

RB-finder: An improved distance-based sliding window method to detect recombination breakpoints

Author keywords

Genotyping; Phylogeny; Recombination detection; Sliding window

Indexed keywords

CONFERENCE PAPER; GENE SEQUENCE; GENETIC RECOMBINATION; GENOTYPE; MATHEMATICAL ANALYSIS; PHYLOGENY; PRIORITY JOURNAL;

EID: 51349120682     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.0154     Document Type: Conference Paper
Times cited : (4)

References (27)
  • 1
    • 0037223888 scopus 로고    scopus 로고
    • The evolutionary genomics of pathogen recombination
    • Awadalla, P. 2003. The evolutionary genomics of pathogen recombination. Nat. Rev. Genet. 4, 50-60.
    • (2003) Nat. Rev. Genet , vol.4 , pp. 50-60
    • Awadalla, P.1
  • 2
    • 0038047665 scopus 로고    scopus 로고
    • Hybrid origin of SIV in chimpanzees
    • Bailes, E., Gao, F., Bibollet-Ruche, F., et al. 2003. Hybrid origin of SIV in chimpanzees. Science 300, 1713.
    • (2003) Science , vol.300 , pp. 1713
    • Bailes, E.1    Gao, F.2    Bibollet-Ruche, F.3
  • 3
    • 1942531897 scopus 로고    scopus 로고
    • Available at:, Accessed July 6, 2008
    • Circulating Recombinant Forms. 2008. Available at: http://hiv-web. lanl.gov/content/hiv-db/CRFs/CRFs.html. Accessed July 6, 2008.
    • Circulating Recombinant Forms. 2008
  • 4
    • 0034791035 scopus 로고    scopus 로고
    • High-resolution haplotype structure in the human genome
    • Daly, M., Andeweg, A., Fouchier, R., et al. 2001. High-resolution haplotype structure in the human genome. Nat. Genet. 29, 229-232.
    • (2001) Nat. Genet , vol.29 , pp. 229-232
    • Daly, M.1    Andeweg, A.2    Fouchier, R.3
  • 5
    • 0024077312 scopus 로고
    • Genetic exchange among natural isolates of bacteria: Recombination within the phoa locus of Escherichia coli
    • DuBose, R., Dykhuisen, D., and Hartl, D. 1988. Genetic exchange among natural isolates of bacteria: recombination within the phoa locus of Escherichia coli. Proc. Natl. Acad. Sci. USA 85, 7036-7040.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 7036-7040
    • DuBose, R.1    Dykhuisen, D.2    Hartl, D.3
  • 6
    • 10744226089 scopus 로고    scopus 로고
    • Recombination following superinfection by HIV-1
    • Fang, G., Weiser, B., Kuiken, C., et al. 2004. Recombination following superinfection by HIV-1. AIDS 18, 153-159.
    • (2004) AIDS , vol.18 , pp. 153-159
    • Fang, G.1    Weiser, B.2    Kuiken, C.3
  • 8
    • 0026640859 scopus 로고
    • Pheotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: Evidence for in vivo recombination and determinants of cytotropism outside the V3 doman
    • Groenink, M., Andeweg, A., Fouchier, R., et al. 1992. Pheotype-associated env gene variation among eight related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 doman. J. Virol. 66, 6175-6180.
    • (1992) J. Virol , vol.66 , pp. 6175-6180
    • Groenink, M.1    Andeweg, A.2    Fouchier, R.3
  • 9
    • 51349124783 scopus 로고    scopus 로고
    • Available at:, Accessed July 6
    • HIV Sequence Database. 2008. Available at: www.hiv.lanl.gov/content/ hiv-db/mainpage.html. Accessed July 6, 2008.
    • (2008) HIV Sequence Database
  • 10
    • 0002459241 scopus 로고    scopus 로고
    • Probabilistic divergence measures for detecting interspecies recombination
    • Husmeier, D., and Wright, F. 2001. Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17, 123-131.
    • (2001) Bioinformatics , vol.17 , pp. 123-131
    • Husmeier, D.1    Wright, F.2
  • 11
    • 18744378862 scopus 로고    scopus 로고
    • Detecting interspecific recombination with a pruned probabilistic divergence measure
    • Husmeier, D., Wright, F., and Milne, I. 2005. Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics 21, 1797-1806.
    • (2005) Bioinformatics , vol.21 , pp. 1797-1806
    • Husmeier, D.1    Wright, F.2    Milne, I.3
  • 12
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
    • (1980) J. Mol. Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 13
    • 0029063822 scopus 로고
    • Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden
    • Leitner, T., Escanilla, D., Marquina, S., et al. 1995. Biological and molecular characterization of subtype D, G, and A/D recombinant HIV-1 transmissions in Sweden. Virology 209, 136-146.
    • (1995) Virology , vol.209 , pp. 136-146
    • Leitner, T.1    Escanilla, D.2    Marquina, S.3
  • 15
    • 33646154660 scopus 로고    scopus 로고
    • Recco: Recombination analysis using cost optimization
    • Maydt, J., and Lengauer, T. 2006. Recco: recombination analysis using cost optimization. Bioinformatics 22, 1064-1071.
    • (2006) Bioinformatics , vol.22 , pp. 1064-1071
    • Maydt, J.1    Lengauer, T.2
  • 16
    • 0034097468 scopus 로고    scopus 로고
    • TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments
    • McGuire, G., and Wright, F. 2000. TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics 16, 130-134.
    • (2000) Bioinformatics , vol.16 , pp. 130-134
    • McGuire, G.1    Wright, F.2
  • 17
    • 0037279717 scopus 로고    scopus 로고
    • Bounds on the minimum number of recombination events in a sample history
    • Myers, S.R., and Griffiths, R.C. 2003. Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375-394.
    • (2003) Genetics , vol.163 , pp. 375-394
    • Myers, S.R.1    Griffiths, R.C.2
  • 18
    • 0037470983 scopus 로고    scopus 로고
    • Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis
    • Paulson, I.T., Banerjei, L., Myers, G.S., et al. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299, 1999-2002.
    • (2003) Science , vol.299 , pp. 1999-2002
    • Paulson, I.T.1    Banerjei, L.2    Myers, G.S.3
  • 19
    • 0036097812 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from data sequences: Empirical data
    • Posada, D. 2002. Evaluation of methods for detecting recombination from data sequences: empirical data. Mol. Biol. Evol. 19, 1198-1212.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1198-1212
    • Posada, D.1
  • 20
    • 0036183042 scopus 로고    scopus 로고
    • The effect of recombination on the accuracy of phylogeny estimation
    • Posada, D., and Crandall, K.R. 2002. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54, 396-402.
    • (2002) J. Mol. Evol , vol.54 , pp. 396-402
    • Posada, D.1    Crandall, K.R.2
  • 21
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D.R., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
    • (1981) Math. Biosci , vol.53 , pp. 131-147
    • Robinson, D.R.1    Foulds, L.R.2
  • 22
    • 3142681466 scopus 로고    scopus 로고
    • A web-based genotyping resource for viral sequences
    • Rozanov, M., Plikat, U., Chappey, C., et al. 2004. A web-based genotyping resource for viral sequences. Nucleic Acids Res. 32, 654-659.
    • (2004) Nucleic Acids Res , vol.32 , pp. 654-659
    • Rozanov, M.1    Plikat, U.2    Chappey, C.3
  • 24
    • 0033793521 scopus 로고    scopus 로고
    • Consequences of recombination on traditional phylogenetic analysis
    • Schierup, M.H., and Hein, J. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
    • (2000) Genetics , vol.156 , pp. 879-891
    • Schierup, M.H.1    Hein, J.2
  • 25
    • 0346252370 scopus 로고    scopus 로고
    • Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: Confirmatory information or additional confusion?
    • Sturmer, M., Doerr, W., and Preiser, W. 2003. Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: Confirmatory information or additional confusion? Curr. Drug Targets Infect. Disord. 3, 373-382.
    • (2003) Curr. Drug Targets Infect. Disord , vol.3 , pp. 373-382
    • Sturmer, M.1    Doerr, W.2    Preiser, W.3
  • 26
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequencing weighting, position specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequencing weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 27
    • 0031892518 scopus 로고    scopus 로고
    • Phylogenetic profiles: A graphical method for detecting genetic recombination in homologous sequences
    • Weiller, G.F. 1998. Phylogenetic profiles: a graphical method for detecting genetic recombination in homologous sequences. Mol. Biol. Evol. 15, 326-335.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 326-335
    • Weiller, G.F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.