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Volumn 3, Issue 1, 2007, Pages 0137-0150

Detecting key structural features within highly recombined genes

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; GENES; ITERATIVE METHODS; MINERS; PHYLOGENETIC; SIGNAL ENCODING;

EID: 33846472969     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030014     Document Type: Article
Times cited : (8)

References (34)
  • 1
    • 0025816587 scopus 로고
    • Interspecies recombinational events during the evolution of altered PBP 2x genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae
    • Laible G, Spratt BG, Hakenbeck R (1991) Interspecies recombinational events during the evolution of altered PBP 2x genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae. Mol Microbiol 5: 1993-2002.
    • (1991) Mol Microbiol , vol.5 , pp. 1993-2002
    • Laible, G.1    Spratt, B.G.2    Hakenbeck, R.3
  • 3
    • 13144252236 scopus 로고    scopus 로고
    • Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
    • Maiden M, Bygraves J, Feil E, Morelli G, Russell J, et al. (1998) Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95: 3140-3145.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3140-3145
    • Maiden, M.1    Bygraves, J.2    Feil, E.3    Morelli, G.4    Russell, J.5
  • 5
    • 0035793056 scopus 로고    scopus 로고
    • Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
    • Feil EJ, Holmes EC, Bessen DE, Chan M-S, Day NPJ, et al. (2001) Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98: 182-187.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 182-187
    • Feil, E.J.1    Holmes, E.C.2    Bessen, D.E.3    Chan, M.-S.4    Day, N.P.J.5
  • 6
    • 13444251528 scopus 로고    scopus 로고
    • RDP2: Recombination detection and analysis from sequence alignments
    • Martin DP, Williamson C, Posada D (2005) RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics 21: 260-262.
    • (2005) Bioinformatics , vol.21 , pp. 260-262
    • Martin, D.P.1    Williamson, C.2    Posada, D.3
  • 7
    • 0034107091 scopus 로고    scopus 로고
    • Emm and sof gene sequence variation in relation to serological typing of opacity factor positive group A streptococci
    • Beall B, Gherardi G, Lovgren M, Forwick B, Facklam R, et al. (2000) Emm and sof gene sequence variation in relation to serological typing of opacity factor positive group A streptococci. Microbiology 146: 1195-1209.
    • (2000) Microbiology , vol.146 , pp. 1195-1209
    • Beall, B.1    Gherardi, G.2    Lovgren, M.3    Forwick, B.4    Facklam, R.5
  • 8
    • 0033066718 scopus 로고    scopus 로고
    • REPuter: Fast computation of maximal repeats in complete genomes
    • Kurtz S, Schleiermacher C (1999) REPuter: Fast computation of maximal repeats in complete genomes. Bioinformatics 15: 426-427.
    • (1999) Bioinformatics , vol.15 , pp. 426-427
    • Kurtz, S.1    Schleiermacher, C.2
  • 9
    • 0037007095 scopus 로고    scopus 로고
    • Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks
    • Smoot JC, Barbian KD, Van Gompel JJ, Smoot LM, Chaussee MS, et al. (2002) Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci U S A 99: 4668-4473.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 4668-4473
    • Smoot, J.C.1    Barbian, K.D.2    Van Gompel, J.J.3    Smoot, L.M.4    Chaussee, M.S.5
  • 10
    • 0024331495 scopus 로고
    • Recruitment of a penicillin-binding protein gene from Neisseria flavescens during the emergence of penicillin resistance in Neisseria meningitidis
    • Spratt BG, Zhang Q, Jones DM, Hutchison A, Brannigan JA (1989) Recruitment of a penicillin-binding protein gene from Neisseria flavescens during the emergence of penicillin resistance in Neisseria meningitidis. Proc Natl Acad Sci U S A 86: 8988-8992.
    • (1989) Proc Natl Acad Sci U S A , vol.86 , pp. 8988-8992
    • Spratt, B.G.1    Zhang, Q.2    Jones, D.M.3    Hutchison, A.4    Brannigan, J.A.5
  • 11
    • 0026708873 scopus 로고
    • Analyzing the mosaic structure of genes
    • Maynard Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
    • (1992) J Mol Evol , vol.34 , pp. 126-129
    • Maynard Smith, J.1
  • 12
    • 0032808466 scopus 로고    scopus 로고
    • BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences (174: 247)
    • Tatusova TA, Madden TL (1999) BLAST 2 SEQUENCES, a new tool for comparing protein and nucleotide sequences (174: 247). FEMS Microbiol Lett 177: 187-188.
    • (1999) FEMS Microbiol Lett , vol.177 , pp. 187-188
    • Tatusova, T.A.1    Madden, T.L.2
  • 14
    • 0033053213 scopus 로고    scopus 로고
    • The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis
    • Holmes EC, Urwin R, Maiden MCJ (1999) The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol Biol Evol 16: 741-749.
    • (1999) Mol Biol Evol , vol.16 , pp. 741-749
    • Holmes, E.C.1    Urwin, R.2    Maiden, M.C.J.3
  • 15
    • 19344363636 scopus 로고    scopus 로고
    • Segmentally variable genes: A new perspective on adaptation
    • Zheng Y, Roberts RJ, Kasif S (2004) Segmentally variable genes: A new perspective on adaptation. PLoS Biol 2 (4): 452-464.
    • (2004) PLoS Biol , vol.2 , Issue.4 , pp. 452-464
    • Zheng, Y.1    Roberts, R.J.2    Kasif, S.3
  • 16
    • 0031764441 scopus 로고    scopus 로고
    • A multilocus sequence typing scheme for Streptococcus pneumoniae: Identification of clones associated with invasive disease
    • Enright MC, Spratt BG (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: Identification of clones associated with invasive disease. Microbiology 144: 3049-3060.
    • (1998) Microbiology , vol.144 , pp. 3049-3060
    • Enright, M.C.1    Spratt, B.G.2
  • 17
    • 0035082969 scopus 로고    scopus 로고
    • Multilocus sequence typing of Streptococcus pyogenes and the relationship between emm-type and clone
    • Enright MC, Spratt BG, Kalia A, Cross JH, Bessen DE (2001) Multilocus sequence typing of Streptococcus pyogenes and the relationship between emm-type and clone. Infect Immun 69: 2416-2427.
    • (2001) Infect Immun , vol.69 , pp. 2416-2427
    • Enright, M.C.1    Spratt, B.G.2    Kalia, A.3    Cross, J.H.4    Bessen, D.E.5
  • 18
    • 0041322724 scopus 로고    scopus 로고
    • Serum opacity factor (SOF) of Streptococcus pyogenes evokes antibodies that opsonize homologous and heterologous SOF-positive serotypes of group A streptococci
    • Courtney HS, Hasty DL, Dale JB (2003) Serum opacity factor (SOF) of Streptococcus pyogenes evokes antibodies that opsonize homologous and heterologous SOF-positive serotypes of group A streptococci. Infection Immunity 71: 5097-5103.
    • (2003) Infection Immunity , vol.71 , pp. 5097-5103
    • Courtney, H.S.1    Hasty, D.L.2    Dale, J.B.3
  • 19
    • 33645061275 scopus 로고    scopus 로고
    • Anti-phagocytic mechanisms of Streptococcus pyogenes: Binding of fibrinogen to M-related protein
    • Courtney HS, Hasty DL, Dale JB (2006) Anti-phagocytic mechanisms of Streptococcus pyogenes: Binding of fibrinogen to M-related protein. Mol Microbiol 59: 936-947.
    • (2006) Mol Microbiol , vol.59 , pp. 936-947
    • Courtney, H.S.1    Hasty, D.L.2    Dale, J.B.3
  • 20
    • 0032910564 scopus 로고    scopus 로고
    • Serum opacity factor is a major fibronectin-binding protein and a virulence determinant of M type 2 Streptococcus pyogenes
    • Courtney HS, Hasty DL, Li Y, Chiang HC, Thacker JL, et al. (1999) Serum opacity factor is a major fibronectin-binding protein and a virulence determinant of M type 2 Streptococcus pyogenes. Mol Microbiol 32: 89-98.
    • (1999) Mol Microbiol , vol.32 , pp. 89-98
    • Courtney, H.S.1    Hasty, D.L.2    Li, Y.3    Chiang, H.C.4    Thacker, J.L.5
  • 21
    • 0037315055 scopus 로고    scopus 로고
    • Molecular genetic analysis of a group A Streptococcus operon encoding serum opacity factor and a novel fibronectin-binding protein, SfbX
    • Jeng A, Sakota V, Li ZY, Datta V, Beall B, et al. (2003) Molecular genetic analysis of a group A Streptococcus operon encoding serum opacity factor and a novel fibronectin-binding protein, SfbX. J Bacteriol 185: 1208-1217.
    • (2003) J Bacteriol , vol.185 , pp. 1208-1217
    • Jeng, A.1    Sakota, V.2    Li, Z.Y.3    Datta, V.4    Beall, B.5
  • 22
    • 0028928762 scopus 로고
    • DNA sequence of the serum opacity factor of group A streptococci: Identification of a fibronectin-binding repeat domain
    • Rakonjac JV, Robbins JC, Fischetti VA (1995) DNA sequence of the serum opacity factor of group A streptococci: Identification of a fibronectin-binding repeat domain. Infect Immun 63: 622-631.
    • (1995) Infect Immun , vol.63 , pp. 622-631
    • Rakonjac, J.V.1    Robbins, J.C.2    Fischetti, V.A.3
  • 23
    • 0032831111 scopus 로고    scopus 로고
    • SfbII protein, a fibronectin binding surface protein of group A streptococci, is a serum opacity factor with high serotype-specific apolipoproteinase activity
    • Kreikemeyer B, Martin DR, Chhatwal GS (1999) SfbII protein, a fibronectin binding surface protein of group A streptococci, is a serum opacity factor with high serotype-specific apolipoproteinase activity. FEMS Microbiol Lett 178: 305-311.
    • (1999) FEMS Microbiol Lett , vol.178 , pp. 305-311
    • Kreikemeyer, B.1    Martin, D.R.2    Chhatwal, G.S.3
  • 24
    • 0032900188 scopus 로고    scopus 로고
    • Report on an international workshop: Demonstration of emm typing and validation of provisional M-types of group A streptococci
    • Facklam R, Beall B, Efstratiou A, Fischetti V, Kaplan E, et al. (1999) Report on an international workshop: Demonstration of emm typing and validation of provisional M-types of group A streptococci. Emerg Infect Dis 5: 247-253.
    • (1999) Emerg Infect Dis , vol.5 , pp. 247-253
    • Facklam, R.1    Beall, B.2    Efstratiou, A.3    Fischetti, V.4    Kaplan, E.5
  • 25
    • 2942630097 scopus 로고    scopus 로고
    • Encoded errors: Mutations and rearrangements mediated by misalignment at repetitive DNA sequences [Review]
    • Lovett ST (2004) Encoded errors: Mutations and rearrangements mediated by misalignment at repetitive DNA sequences [Review]. Mol Microbiol 52: 1243-1253.
    • (2004) Mol Microbiol , vol.52 , pp. 1243-1253
    • Lovett, S.T.1
  • 26
    • 0037133288 scopus 로고    scopus 로고
    • Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae
    • Prudhomme M, Libante V, Claverys JP (2002) Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 99: 2100-2105.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 2100-2105
    • Prudhomme, M.1    Libante, V.2    Claverys, J.P.3
  • 27
    • 13244262636 scopus 로고    scopus 로고
    • Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome
    • Sekizaki T, Takamatsu D, Osaki M, Shimoji Y (2005) Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome. J Bacteriol 187: 872-883.
    • (2005) J Bacteriol , vol.187 , pp. 872-883
    • Sekizaki, T.1    Takamatsu, D.2    Osaki, M.3    Shimoji, Y.4
  • 29
    • 3042662429 scopus 로고    scopus 로고
    • Multi-locus sequence typing of Streptococcus pyogenes, representing most known emm-types and distinctions among sub-population genetic structures
    • McGregor KF, Spratt BG, Kalia A, Bennett A, Bilek N, et al. (2004) Multi-locus sequence typing of Streptococcus pyogenes, representing most known emm-types and distinctions among sub-population genetic structures. J Bacteriol 186: 4285-4294.
    • (2004) J Bacteriol , vol.186 , pp. 4285-4294
    • McGregor, K.F.1    Spratt, B.G.2    Kalia, A.3    Bennett, A.4    Bilek, N.5
  • 31
    • 0028961935 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates (11: 459)
    • Kuhner MK, Felsenstein J (1995) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates (11: 459). Mol Biol Evol 12: 525.
    • (1995) Mol Biol Evol , vol.12 , pp. 525
    • Kuhner, M.K.1    Felsenstein, J.2
  • 32
    • 33846545094 scopus 로고    scopus 로고
    • Hall TA (1999) BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
    • Hall TA (1999) BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
  • 33
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 34
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method or rapid multiple sequence alignment based on fast Fourier transform
    • Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: A novel method or rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.