메뉴 건너뛰기




Volumn 27, Issue 11, 2011, Pages 1466-1472

Alignment-free detection of local similarity among viral and bacterial genomes

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 79957873906     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr176     Document Type: Article
Times cited : (47)

References (30)
  • 2
    • 0024988375 scopus 로고
    • Protein database searches for multiple alignments
    • Altschul,S.F. and Lipman,D.J. (1990) Protein database searches for multiple alignments. Proc. Natl Acad. Sci. USA 87, 5509-5513.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 5509-5513
    • Altschul, S.F.1    Lipman, D.J.2
  • 3
    • 75449094838 scopus 로고    scopus 로고
    • Sequences and consequences
    • Brenner,S. (2010) Sequences and consequences. Phil. Trans. R. Soc. B, 365, 207-212.
    • (2010) Phil. Trans. R. Soc. B , vol.365 , pp. 207-212
    • Brenner, S.1
  • 4
    • 28944454501 scopus 로고    scopus 로고
    • DNAassembly with gaps (Dawg): simulating sequence evolution
    • Cartwright,R. (2005) DNAassembly with gaps (Dawg): simulating sequence evolution. Bioinformatics, 21 (Suppl. 3), iii31-iii38.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 3
    • Cartwright, R.1
  • 5
    • 34249027580 scopus 로고    scopus 로고
    • Inference of bacterial microevolution using multilocus sequence data
    • Didelot,X. and Falush,D. (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics, 175, 1251-1266.
    • (2007) Genetics , vol.175 , pp. 1251-1266
    • Didelot, X.1    Falush, D.2
  • 6
    • 79251573854 scopus 로고    scopus 로고
    • Inference of homologous recombination in bacteria using whole genome sequences
    • Didelot,X. et al. (2010) Inference of homologous recombination in bacteria using whole genome sequences. Genetics, 186, 1435-1449.
    • (2010) Genetics , vol.186 , pp. 1435-1449
    • Didelot, X.1
  • 7
    • 75849146491 scopus 로고    scopus 로고
    • Efficient estimation of pairwise distances between genomes
    • Domazet-Lošo,M. and Haubold,B. (2009) Efficient estimation of pairwise distances between genomes. Bioinformatics, 25, 3221-3227.
    • (2009) Bioinformatics , vol.25 , pp. 3221-3227
    • Domazet-Lošo, M.1    Haubold, B.2
  • 8
    • 0000122573 scopus 로고
    • PHYLIP - phylogeny inference package (Version 3.2)
    • Felsenstein,J. (1989) PHYLIP - phylogeny inference package (Version 3.2). Cladistics, 5, 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 9
    • 84979917497 scopus 로고    scopus 로고
    • Compressed text indexes: from theory to practice
    • Ferragina,P. et al. (2008) Compressed text indexes: from theory to practice. ACMJ.Exp. Algorithmics, 13, 1.12:1-1.12:31.
    • (2008) ACMJ.Exp. Algorithmics , vol.13
    • Ferragina, P.1
  • 10
    • 79951527464 scopus 로고    scopus 로고
    • Alignment-free estimation of nucleotide diversity
    • Haubold,B. (2011) Alignment-free estimation of nucleotide diversity. Bioinformatics, 17, 449-455.
    • (2011) Bioinformatics , vol.17 , pp. 449-455
    • Haubold, B.1
  • 11
  • 12
    • 25444513996 scopus 로고    scopus 로고
    • Genome comparison without alignment using shortest unique substrings
    • Haubold,B. et al. (2005) Genome comparison without alignment using shortest unique substrings. BMC Bioinformatics, 6, 123.
    • (2005) BMC Bioinformatics , vol.6 , pp. 123
    • Haubold, B.1
  • 13
    • 70349789710 scopus 로고    scopus 로고
    • Estimating mutation distances from unaligned genomes
    • Haubold,B. et al. (2009) Estimating mutation distances from unaligned genomes. J. Comput. Biol., 16, 1487-1500.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1487-1500
    • Haubold, B.1
  • 14
    • 34247846229 scopus 로고    scopus 로고
    • The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E.coli genomes
    • Johnson,T. et al. (2007) The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E.coli genomes. J. Bacteriol., 189, 3228-3236.
    • (2007) J. Bacteriol. , vol.189 , pp. 3228-3236
    • Johnson, T.1
  • 15
    • 73449085165 scopus 로고    scopus 로고
    • An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1
    • Kosakovsky Pond,S.L. et al. (2009) An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput. Biol., 5, e1000581.
    • (2009) PLoS Comput. Biol. , vol.5
    • Kosakovsky Pond, S.L.1
  • 16
    • 77951115860 scopus 로고    scopus 로고
    • Detecting genomic islands using bioinformatics approaches
    • Langille,M.G.I. (2010) Detecting genomic islands using bioinformatics approaches.Nat. Rev. Microbiol., 8, 373-382.
    • (2010) Nat. Rev. Microbiol. , vol.8 , pp. 373-382
    • Langille, M.G.I.1
  • 17
    • 25144458435 scopus 로고    scopus 로고
    • Technical Report LA-UR 06-0680, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM
    • Leitner,T. et al. (2005) HIV sequence compendium. Technical Report LA-UR 06-0680, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM.
    • (2005) HIV sequence compendium
    • Leitner, T.1
  • 18
    • 77953537274 scopus 로고    scopus 로고
    • A multiplex PCR method to detect 14 Escherichia coli serogroups associated with urinary tract infectcions
    • Li,D. et al. (2010) A multiplex PCR method to detect 14 Escherichia coli serogroups associated with urinary tract infectcions. J. Microbiol. Methods, 82, 71-77.
    • (2010) J. Microbiol. Methods , vol.82 , pp. 71-77
    • Li, D.1
  • 20
    • 0026025364 scopus 로고
    • Localized sex in bacteria
    • Maynard Smith,J. et al. (1991) Localized sex in bacteria. Nature, 349, 29-31.
    • (1991) Nature , vol.349 , pp. 29-31
    • Maynard Smith, J.1
  • 21
    • 0025133386 scopus 로고
    • Molecular evolution of the Escherichia coli chromosome. III. Clonal frames
    • Milkman,R. and McKane Bridges,M. (1990) Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics, 126, 505-517.
    • (1990) Genetics , vol.126 , pp. 505-517
    • Milkman, R.1    McKane Bridges, M.2
  • 22
    • 0014757386 scopus 로고
    • Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 23
    • 34147144193 scopus 로고    scopus 로고
    • A taxonomy of suffix array construction algorithms
    • Puglisi,S.J. et al. (2007) A taxonomy of suffix array construction algorithms. ACM Comput. Surv., 39,4.
    • (2007) ACM Comput. Surv. , vol.39 , pp. 4
    • Puglisi, S.J.1
  • 24
    • 75149164526 scopus 로고    scopus 로고
    • Alignment-free sequence comparison (i): statistics and power
    • Reinert,G. et al. (2009) Alignment-free sequence comparison (i): statistics and power. J. Comput. Biol., 16, 1615-1634.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1615-1634
    • Reinert, G.1
  • 25
    • 3142681466 scopus 로고    scopus 로고
    • Aweb-based genotyping resource for viral sequences
    • Rozanov,M. et al. (2004)Aweb-based genotyping resource for viral sequences. Nucleic Acids Res., 32, W654-W659.
    • (2004) Nucleic Acids Res. , vol.32
    • Rozanov, M.1
  • 26
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 27
    • 25444524604 scopus 로고    scopus 로고
    • Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'
    • Tettelin,H. et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc. Natl Acad. Sci. USA, 102, 13950-13955.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13950-13955
    • Tettelin, H.1
  • 28
    • 0037342499 scopus 로고    scopus 로고
    • Alignment-free sequence comparison-a review
    • Vinga,S. and Almeida,J. (2003) Alignment-free sequence comparison-a review. Bioinformatics, 19, 513-523.
    • (2003) Bioinformatics , vol.19 , pp. 513-523
    • Vinga, S.1    Almeida, J.2
  • 29
    • 63549098393 scopus 로고    scopus 로고
    • Accurate detection of recombinant breakpoints in whole-genome alignments
    • Westesson,O. and Holmes,I. (2009) Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput. Biol., 5, e1000318-e1000318.
    • (2009) PLoS Comput. Biol. , vol.5
    • Westesson, O.1    Holmes, I.2
  • 30
    • 34547886848 scopus 로고    scopus 로고
    • Nucleotide composition string selection in HIV-1 subtyping using whole genomes
    • Wu,X. et al. (2007) Nucleotide composition string selection in HIV-1 subtyping using whole genomes. Bioinformatics, 23, 1744-1752.
    • (2007) Bioinformatics , vol.23 , pp. 1744-1752
    • Wu, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.