메뉴 건너뛰기




Volumn 23, Issue 14, 2007, Pages 1744-1752

Nucleotide composition string selection in HIV-1 subtyping using whole genomes

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

EID: 34547886848     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm248     Document Type: Article
Times cited : (47)

References (29)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 27544496497 scopus 로고    scopus 로고
    • An automated genotyping system for analysis of HIV-1 and other microbial sequences
    • deOliveira,T. et al. (2005) An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics, 21, 3797-3800.
    • (2005) Bioinformatics , vol.21 , pp. 3797-3800
    • deOliveira, T.1
  • 4
    • 4944257028 scopus 로고    scopus 로고
    • Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
    • Dopazo,H. et al. (2004) Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. Bioinformatics, 20, i116-i121.
    • (2004) Bioinformatics , vol.20
    • Dopazo, H.1
  • 5
    • 33746192134 scopus 로고    scopus 로고
    • Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity
    • Gifford,R. et al. (2006) Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 20, 1521-1529.
    • (2006) AIDS , vol.20 , pp. 1521-1529
    • Gifford, R.1
  • 6
    • 0000100455 scopus 로고
    • A new challenge for compression algorithms: Genetic sequences
    • Grumbach,S. and Tahi,F. (1994) A new challenge for compression algorithms: Genetic sequences. J. Inf. Proces. Manage., 30, 875-866.
    • (1994) J. Inf. Proces. Manage , vol.30 , pp. 875-866
    • Grumbach, S.1    Tahi, F.2
  • 7
    • 84960450653 scopus 로고    scopus 로고
    • Prokaryote phylogeny without sequence alignment: From avoidance signature to composition distance
    • Hao,B. and Qi,J. (2003) Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. In Proceedings of the 2003 IEEE Bioinformatics Conference (CSB 2003), pp. 375-385.
    • (2003) Proceedings of the 2003 IEEE Bioinformatics Conference (CSB 2003) , pp. 375-385
    • Hao, B.1    Qi, J.2
  • 8
    • 0034864707 scopus 로고    scopus 로고
    • Use of whole genome sequence data to infer baculovirus phylogeny
    • Herniou,E. et al. (2001) Use of whole genome sequence data to infer baculovirus phylogeny. J. Virol., 75, 8117-8126.
    • (2001) J. Virol , vol.75 , pp. 8117-8126
    • Herniou, E.1
  • 9
    • 0036218557 scopus 로고    scopus 로고
    • Using homolog groups to create a whole-genomic tree of free-living organisms: An update
    • House,C. and Fitz-Gibbon,S. (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: An update. Mol. Evol. 54, 539-547.
    • (2002) Mol. Evol , vol.54 , pp. 539-547
    • House, C.1    Fitz-Gibbon, S.2
  • 10
    • 0029060923 scopus 로고
    • Dinucleotide relative abundance extremes: A genomic, signature
    • Karlin,S. and Burge,C. (1995) Dinucleotide relative abundance extremes: a genomic, signature. Trends Genet., 11, 283-290.
    • (1995) Trends Genet , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 12
    • 0036034976 scopus 로고    scopus 로고
    • Phylogeny based on whole genome as inferred from complete information set analysis
    • Li,W. et al. (2002) Phylogeny based on whole genome as inferred from complete information set analysis. J. Biol. Phy., 28, 439-447.
    • (2002) J. Biol. Phy , vol.28 , pp. 439-447
    • Li, W.1
  • 13
    • 13444251528 scopus 로고    scopus 로고
    • RDP2: Recombination detection and analysis from sequence alignments
    • Martin,D.P. et al. (2005) RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics, 21, 260-262.
    • (2005) Bioinformatics , vol.21 , pp. 260-262
    • Martin, D.P.1
  • 14
    • 4444299144 scopus 로고    scopus 로고
    • TOPLi: Software for automatic identification of recombinant sequences within DNA multiple alignments
    • Milne,I. et al. (2004) TOPLi: Software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics, 20, 1806-1807.
    • (2004) Bioinformatics , vol.20 , pp. 1806-1807
    • Milne, I.1
  • 16
    • 24144500828 scopus 로고    scopus 로고
    • A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)
    • Myers,R.E. et al. (2005) A statistical model for HIV-1 sequence classification using the subtype analyser (STAR) Bioinformatics, 21, 3535-3540.
    • (2005) Bioinformatics , vol.21 , pp. 3535-3540
    • Myers, R.E.1
  • 17
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach
    • Qi,J. et al. (2004) Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach. J. Mol. Evol. 58, 1-11.
    • (2004) J. Mol. Evol , vol.58 , pp. 1-11
    • Qi, J.1
  • 18
    • 0347989161 scopus 로고    scopus 로고
    • The causes and consequences of HIV evolution
    • Rambaut,A. et al. (2004) The causes and consequences of HIV evolution. Nat. Rev. Gene., 5, 52-61.
    • (2004) Nat. Rev. Gene , vol.5 , pp. 52-61
    • Rambaut, A.1
  • 19
    • 0029852415 scopus 로고    scopus 로고
    • Compression and genetic sequences analysis
    • Rivals,E. et al. (1996) Compression and genetic sequences analysis. Biochimie, 78, 315-322.
    • (1996) Biochimie , vol.78 , pp. 315-322
    • Rivals, E.1
  • 20
    • 3142681466 scopus 로고    scopus 로고
    • A web-based genotyping resource for viral sequences
    • Rozanov,M. et al. (2004) A web-based genotyping resource for viral sequences. Nucleic Acids Res., 32, W654-W659.
    • (2004) Nucleic Acids Res , vol.32
    • Rozanov, M.1
  • 21
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. and Evol., 4 406-425.
    • (1987) Mol. Biol. and Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 22
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • Snel,B. et al. (1999) Genome phylogeny based on gene content. Nat. Genet., 21, 108-110.
    • (1999) Nat. Genet , vol.21 , pp. 108-110
    • Snel, B.1
  • 23
    • 0033621536 scopus 로고    scopus 로고
    • Genome evolution: Gene fusion versus gene fission
    • Snel,B. et al. (2000) Genome evolution: Gene fusion versus gene fission. Trends Genet., 16, 9-11.
    • (2000) Trends Genet , vol.16 , pp. 9-11
    • Snel, B.1
  • 24
    • 4043169069 scopus 로고    scopus 로고
    • A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space
    • Stuart,G. and Berry,M. (2003) A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space. J. Bioinform. and Comput. Biol., 1, 475-493.
    • (2003) J. Bioinform. and Comput. Biol , vol.1 , pp. 475-493
    • Stuart, G.1    Berry, M.2
  • 25
    • 0036213976 scopus 로고    scopus 로고
    • A comprehensive vertebrate phylogeny using vector representation of protein sequences from whole genomes
    • Stuart,G. et al. (2002a) A comprehensive vertebrate phylogeny using vector representation of protein sequences from whole genomes. Mol. Biol. Evol., 19, 554-562.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 554-562
    • Stuart, G.1
  • 26
    • 0036166508 scopus 로고    scopus 로고
    • Integrated gene and species phylogenies from unaligned whole genome sequence
    • Stuart,G. et al. (2002b) Integrated gene and species phylogenies from unaligned whole genome sequence. Bioinformatics, 18, 100-108.
    • (2002) Bioinformatics , vol.18 , pp. 100-108
    • Stuart, G.1
  • 27
    • 4043104082 scopus 로고    scopus 로고
    • A whole genome perspective on the phylogeny of the plant virus family tombusviridae
    • Stuart,G. et al. (2004) A whole genome perspective on the phylogeny of the plant virus family tombusviridae. Arch. Viro., 149, 1595-1610.
    • (2004) Arch. Viro , vol.149 , pp. 1595-1610
    • Stuart, G.1
  • 28
    • 0035887459 scopus 로고    scopus 로고
    • Molecular classification of human carcinomas by use of gene expression signatures
    • Su,A.I. et al. (2001) Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res., 61, 7388-7393.
    • (2001) Cancer Res , vol.61 , pp. 7388-7393
    • Su, A.I.1
  • 29
    • 33748796945 scopus 로고    scopus 로고
    • Whole genome phylogeny construction via complete composition vectors
    • Wu,X. et al. (2006) Whole genome phylogeny construction via complete composition vectors. Int. J. Bioinform. Res. Appl., 2 219-248.
    • (2006) Int. J. Bioinform. Res. Appl , vol.2 , pp. 219-248
    • Wu, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.