메뉴 건너뛰기




Volumn 3, Issue , 2002, Pages

Boostrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RIBOSOME RNA;

EID: 9144225618     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-3-4     Document Type: Article
Times cited : (487)

References (57)
  • 1
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 1977, 74: 5088-5090
    • (1977) Proc. Natl. Acad. Sci. U S A , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 2
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese CR: Bacterial evolution. Microbiol Rev 1987, 51: 221-271
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 4
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF: Phylogenetic classification and the universal tree. Science 1999, 284: 2124-2129
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 6
    • 0031769997 scopus 로고    scopus 로고
    • Evolutionary anomalies among the aminoacyl-tRNA synthetases
    • Doolittle RF, Handy J: Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr Opin Genet Dev 1998, 8: 630-636
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 630-636
    • Doolittle, R.F.1    Handy, J.2
  • 7
    • 0030868589 scopus 로고    scopus 로고
    • Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
    • Koonin EV, Mushegian AR, Galperin MY, Walker DR: Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol 1997, 25: 619-637
    • (1997) Mol. Microbiol. , vol.25 , pp. 619-637
    • Koonin, E.V.1    Mushegian, A.R.2    Galperin, M.Y.3    Walker, D.R.4
  • 8
    • 0034542621 scopus 로고    scopus 로고
    • Horizontal transfer of archaeal genes into the deinococcaceae: Detection by molecular and computer-based approaches
    • Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP: Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches. J Mol Evol 2000, 51: 587-599
    • (2000) J. Mol. Evol. , vol.51 , pp. 587-599
    • Olendzenski, L.1    Liu, L.2    Zhaxybayeva, O.3    Murphey, R.4    Shin, D.G.5    Gogarten, J.P.6
  • 10
    • 0035225012 scopus 로고    scopus 로고
    • Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    • research0033.1-research0033.14
    • Makarova KS, Ponomarev VA, Koonin EV: Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol 2001, 2: research0033.1-0033.14
    • (2001) Genome Biol. , vol.2
    • Makarova, K.S.1    Ponomarev, V.A.2    Koonin, E.V.3
  • 11
    • 0034565944 scopus 로고    scopus 로고
    • The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
    • Brochier C, Philippe H, Moreira D: The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet 2000, 16: 529-533
    • (2000) Trends Genet. , vol.16 , pp. 529-533
    • Brochier, C.1    Philippe, H.2    Moreira, D.3
  • 12
    • 0032830481 scopus 로고    scopus 로고
    • Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    • Wolf YI, Aravind L, Grishin NV, Koonin EV: Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 1999, 9: 689-710
    • (1999) Genome Res. , vol.9 , pp. 689-710
    • Wolf, Y.I.1    Aravind, L.2    Grishin, N.V.3    Koonin, E.V.4
  • 14
    • 0032778047 scopus 로고    scopus 로고
    • The genomic tree as revealed from whole proteome comparisons
    • Tekaia F, Lazcano A, Dujon B: The genomic tree as revealed from whole proteome comparisons. Genome Res 1999, 9: 550-557
    • (1999) Genome Res. , vol.9 , pp. 550-557
    • Tekaia, F.1    Lazcano, A.2    Dujon, B.3
  • 15
    • 0032900532 scopus 로고    scopus 로고
    • Genome phylogeny based on gene content
    • [see comments]
    • Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content [see comments]. Nat Genet 1999, 21: 108-110
    • (1999) Nat. Genet. , vol.21 , pp. 108-110
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 16
    • 0033231209 scopus 로고    scopus 로고
    • Whole genome-based phylogenetic analysis of free-living microorganisms
    • Fitz-Gibbon ST, House CH: Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 1999, 27: 4218-4222
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4218-4222
    • Fitz-Gibbon, S.T.1    House, C.H.2
  • 17
    • 0033918311 scopus 로고    scopus 로고
    • Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
    • Lin J, Gerstein M: Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 2000, 10: 808-818
    • (2000) Genome Res. , vol.10 , pp. 808-818
    • Lin, J.1    Gerstein, M.2
  • 20
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 1990, 87: 4576-4579
    • (1990) Proc. Natl. Acad. Sci. U S A , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 21
    • 0031678692 scopus 로고    scopus 로고
    • SplitsTree: Analyzing and visualizing evolutionary data
    • Huson DH: SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 1998, 14: 68-73
    • (1998) Bioinformatics , vol.14 , pp. 68-73
    • Huson, D.H.1
  • 22
    • 0031828312 scopus 로고    scopus 로고
    • The mosaic nature of the eukaryotic nucleus
    • Ribeiro S, Golding GB: The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 1998, 15: 779-788
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 779-788
    • Ribeiro, S.1    Golding, G.B.2
  • 24
    • 0031002417 scopus 로고    scopus 로고
    • Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
    • Strimmer K, von Haeseler A: Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 1997, 94: 6815-6819
    • (1997) Proc. Natl. Acad. Sci. U S A , vol.94 , pp. 6815-6819
    • Strimmer, K.1    von Haeseler, A.2
  • 25
    • 0030623948 scopus 로고    scopus 로고
    • SEALS: A system for easy analysis of lots of sequences
    • Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences. ISMB 1997, 5: 333-339
    • (1997) ISMB , vol.5 , pp. 333-339
    • Walker, D.R.1    Koonin, E.V.2
  • 26
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278: 631-637
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 27
    • 0033956060 scopus 로고    scopus 로고
    • The COG database: A tool for genome-scale analysis of protein functions and evolution
    • Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28: 33-36
    • (2000) Nucleic Acids Res. , vol.28 , pp. 33-36
    • Tatusov, R.L.1    Galperin, M.Y.2    Natale, D.A.3    Koonin, E.V.4
  • 30
    • 0029933671 scopus 로고    scopus 로고
    • Effective protein sequence comparison
    • Pearson WR: Effective protein sequence comparison. Methods Enzymol 1996, 266: 227-258
    • (1996) Methods Enzymol. , vol.266 , pp. 227-258
    • Pearson, W.R.1
  • 31
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F: MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17: 754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 32
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39: 783-791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 34
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B, Yang Z: Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 1996, 43:304-311
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 36
    • 0033598755 scopus 로고    scopus 로고
    • Recurrent invasion and extinction of a selfish gene
    • Goddard MR, Burt A: Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci U S A 1999, 96: 13880-13885
    • (1999) Proc. Natl. Acad. Sci. U S A , vol.96 , pp. 13880-13885
    • Goddard, M.R.1    Burt, A.2
  • 37
    • 0032540298 scopus 로고    scopus 로고
    • Witnessing the evolution of transcription in mitochondria: The mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase
    • Rousvoal S, Oudot M, Fontaine J, Kloareg B, Goer SL: Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase. J Mol Biol 1998, 277: 1047-1057
    • (1998) J. Mol. Biol. , vol.277 , pp. 1047-1057
    • Rousvoal, S.1    Oudot, M.2    Fontaine, J.3    Kloareg, B.4    Goer, S.L.5
  • 39
    • 0024601035 scopus 로고
    • Mitochondrial RNA polymerase: Dual role in transcription and replication
    • Schinkel AH, Tabak HF: Mitochondrial RNA polymerase: dual role in transcription and replication. Trends Genet 1989, 5: 149-154
    • (1989) Trends Genet. , vol.5 , pp. 149-154
    • Schinkel, A.H.1    Tabak, H.F.2
  • 40
    • 0031865507 scopus 로고    scopus 로고
    • Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria
    • Gupta RS, Johari V: Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria. J Mol Evol 1998, 46: 716-720
    • (1998) J. Mol. Evol. , vol.46 , pp. 716-720
    • Gupta, R.S.1    Johari, V.2
  • 41
    • 0033030130 scopus 로고    scopus 로고
    • Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis
    • Gupta RS, Mukhtar T, Singh B: Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol Microbiol 1999, 32: 893-906
    • (1999) Mol. Microbiol. , vol.32 , pp. 893-906
    • Gupta, R.S.1    Mukhtar, T.2    Singh, B.3
  • 42
    • 0033935581 scopus 로고    scopus 로고
    • The natural evolutionary relationships among prokaryotes
    • Gupta RS: The natural evolutionary relationships among prokaryotes. Crit Rev Microbiol 2000, 26: 111-131
    • (2000) Crit. Rev. Microbiol. , vol.26 , pp. 111-131
    • Gupta, R.S.1
  • 43
    • 0034622999 scopus 로고    scopus 로고
    • Molecular evidence for the early evolution of photosynthesis
    • Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE: Molecular evidence for the early evolution of photosynthesis. Science 2000, 289: 1724-1730
    • (2000) Science , vol.289 , pp. 1724-1730
    • Xiong, J.1    Fischer, W.M.2    Inoue, K.3    Nakahara, M.4    Bauer, C.E.5
  • 45
    • 0036137155 scopus 로고    scopus 로고
    • Eubacterial phylogeny based on translational apparatus proteins
    • Brochier C, Bapteste E, Moreira D, Philippe H: Eubacterial phylogeny based on translational apparatus proteins. Trends Genet 2002, 18: 1-5
    • (2002) Trends Genet. , vol.18 , pp. 1-5
    • Brochier, C.1    Bapteste, E.2    Moreira, D.3    Philippe, H.4
  • 46
  • 47
    • 0034780910 scopus 로고    scopus 로고
    • Horizontal gene transfer in prokaryotes: Quantification and classification
    • Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55: 709-742
    • (2001) Annu. Rev. Microbiol. , vol.55 , pp. 709-742
    • Koonin, E.V.1    Makarova, K.S.2    Aravind, L.3
  • 48
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein J: Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 1978, 27: 401-410
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 49
    • 0031793259 scopus 로고    scopus 로고
    • Cloning and sequencing of the homologues of both the bacterial and eukaryotic initiation factor genes (hIF-2 and heIF-2 gamma) from archaeal Halobacterium halobium
    • Hasegawa Y, Sawaoka N, Kado N, Ochi M, Itoh T: Cloning and sequencing of the homologues of both the bacterial and eukaryotic initiation factor genes (hIF-2 and heIF-2 gamma) from archaeal Halobacterium halobium. Biochem Mol Biol Int 1998, 46: 495-507
    • (1998) Biochem. Mol. Biol. Int. , vol.46 , pp. 495-507
    • Hasegawa, Y.1    Sawaoka, N.2    Kado, N.3    Ochi, M.4    Itoh, T.5
  • 50
    • 0029847554 scopus 로고    scopus 로고
    • Selfish operons: Horizontal transfer may drive the evolution of gene clusters
    • Lawrence JG, Roth JR: Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143: 1843-1860
    • (1996) Genetics , vol.143 , pp. 1843-1860
    • Lawrence, J.G.1    Roth, J.R.2
  • 53
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 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
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 54
    • 0034894278 scopus 로고    scopus 로고
    • PAL: An object-oriented programming library for molecular evolution and phylogenetics
    • Drummond A, Strimmer K: PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001, 17: 662-663
    • (2001) Bioinformatics , vol.17 , pp. 662-663
    • Drummond, A.1    Strimmer, K.2
  • 55
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. CABIOS 1992, 8: 275-282
    • (1992) CABIOS , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 56
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: Quartet A maximum-likelihood method for reconstructing tree topologies
    • Strimmer K, von Haeseler A: Quartet puzzling: quartet A maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 1996, 964-969
    • (1996) Molecular Biology and Evolution , pp. 964-969
    • Strimmer, K.1    von Haeseler, A.2
  • 57
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994, 39: 306-314
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.