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Volumn 5, Issue , 2004, Pages

Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL CHROMOSOMES; BACTERIAL GENOMES; GENOME ORGANIZATION; MONONUCLEOTIDES; OLIGONUCLEOTIDE FREQUENCIES; PROCHLOROCOCCUS; USAGE PATTERNS; XYLELLA FASTIDIOSA;

EID: 13244279471     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-90     Document Type: Article
Times cited : (44)

References (47)
  • 2
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • Karlin S: Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 2001, 9:335-343.
    • (2001) Trends Microbiol. , vol.9 , pp. 335-343
    • Karlin, S.1
  • 4
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin S, Mrazek J, Campbell A: Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997, 179:3899-3913.
    • (1997) J. Bacteriol. , vol.179 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.3
  • 5
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ: Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 2003, 13:145-155.
    • (2003) Genome Res. , vol.13 , pp. 145-155
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 6
    • 0034534314 scopus 로고    scopus 로고
    • Visualization of pathogenicity regions in bacteria
    • Friis C, Jensen LJ, Ussery DW: Visualization of pathogenicity regions in bacteria. Genetica 2000, 108: 7-51.
    • (2000) Genetica , vol.108 , pp. 47-51
    • Friis, C.1    Jensen, L.J.2    Ussery, D.W.3
  • 8
    • 0002576679 scopus 로고    scopus 로고
    • Identification of horizontally acquired elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis
    • Pride DT, Blaser MJ: Identification of horizontally acquired elements in Helicobacter pylori and other prokaryotes using oligonucleotide difference analysis. Genome Lett 2002, 1:2-15.
    • (2002) Genome Lett. , vol.1 , pp. 2-15
    • Pride, D.T.1    Blaser, M.J.2
  • 11
    • 0032173634 scopus 로고    scopus 로고
    • Global dinucleotide signatures and analysis of genomic heterogeneity
    • Karlin S: Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1998, 1: 98-610.
    • (1998) Curr. Opin. Microbiol. , vol.1 , pp. 598-610
    • Karlin, S.1
  • 12
    • 0036677661 scopus 로고    scopus 로고
    • Why are complementary DNA strands symmetric?
    • Baisne P-F, Hampson S, Baldi P: Why are complementary DNA strands symmetric? Bioinformatics 2002, 18:1021-1033.
    • (2002) Bioinformatics , vol.18 , pp. 1021-1033
    • Baisne, P.-F.1    Hampson, S.2    Baldi, P.3
  • 13
    • 0033639086 scopus 로고    scopus 로고
    • Sequence analysis by additive scales: DNA structure for sequences and repeats of all length
    • Baldi P, Baisne P-F: Sequence analysis by additive scales: DNA structure for sequences and repeats of all length. Bioinformatics 2000, 16:865-889.
    • (2000) Bioinformatics , vol.16 , pp. 865-889
    • Baldi, P.1    Baisne, P.-F.2
  • 14
    • 0000724617 scopus 로고
    • Structure and function of nucleic acids as cell constituents
    • Chargaff E: Structure and function of nucleic acids as cell constituents. Fed Proc 1951, 10:344-360.
    • (1951) Fed. Proc. , vol.10 , pp. 344-360
    • Chargaff, E.1
  • 15
    • 0042814847 scopus 로고    scopus 로고
    • Methods for comparing sources of strand compositional asymmetry in microbial chromosomes
    • Baran RH, Ko H, Jernigan RW: Methods for comparing sources of strand compositional asymmetry in microbial chromosomes. DNA Res 2003, 30:85-95.
    • (2003) DNA Res. , vol.30 , pp. 85-95
    • Baran, R.H.1    Ko, H.2    Jernigan, R.W.3
  • 16
    • 0033935187 scopus 로고    scopus 로고
    • The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
    • Tillier ER, Collins RA: The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 2000, 50: 49-257.
    • (2000) J. Mol. Evol. , vol.50 , pp. 249-257
    • Tillier, E.R.1    Collins, R.A.2
  • 17
    • 0018143102 scopus 로고
    • An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking
    • Ornstein RL, Rein R, Breen DL, MacElroy RD: An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 1978, 17: 341-2360.
    • (1978) Biopolymers , vol.17 , pp. 2341-2360
    • Ornstein, R.L.1    Rein, R.2    Breen, D.L.3    MacElroy, R.D.4
  • 18
    • 0030003963 scopus 로고    scopus 로고
    • Propeller twist of base-pairs and the conformational mobility of dinucleotide steps in DNA
    • Hassan MAE, Calladine CR: Propeller twist of base-pairs and the conformational mobility of dinucleotide steps in DNA. J Mol Biol 1996, 259:95-103.
    • (1996) J. Mol. Biol. , vol.259 , pp. 95-103
    • Hassan, M.A.E.1    Calladine, C.R.2
  • 21
    • 0029039118 scopus 로고
    • Sequence-dependent bending propensity of DNA as reveald by DNase I: Parameters for trinucleotides
    • Brukner I, Sánchez R, Suck D, Pongor S: Sequence-dependent bending propensity of DNA as reveald by DNase I: parameters for trinucleotides. EMBO J 1995, 14:1812-1818.
    • (1995) EMBO J. , vol.14 , pp. 1812-1818
    • Brukner, I.1    Sánchez, R.2    Suck, D.3    Pongor, S.4
  • 22
    • 0026758856 scopus 로고
    • Base compositional structure of genomes
    • Fickett JW, Torney DC, Wolf DR: Base compositional structure of genomes. Genomics 1992, 13:1056-1064.
    • (1992) Genomics , vol.13 , pp. 1056-1064
    • Fickett, J.W.1    Torney, D.C.2    Wolf, D.R.3
  • 23
    • 0028828990 scopus 로고
    • Relative role of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species
    • Forsdyke DR: Relative role of primary sequence and (G+C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J Mol Evol 1995, 41:573-581.
    • (1995) J. Mol. Evol. , vol.41 , pp. 573-581
    • Forsdyke, D.R.1
  • 24
    • 0034125366 scopus 로고    scopus 로고
    • Probabilistic and statistical properties of words: An overview
    • Reinert G, Schbath S, Waterman MS: Probabilistic and statistical properties of words: an overview. J Comp Biol 2000, 7:1-46.
    • (2000) J. Comp. Biol. , vol.7 , pp. 1-46
    • Reinert, G.1    Schbath, S.2    Waterman, M.S.3
  • 26
    • 0347285389 scopus 로고    scopus 로고
    • Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C
    • Klockgether J, Reva O, Larbig K, Tümmler B: Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C. J Bacteriol 2004, 186:518-534.
    • (2004) J. Bacteriol. , vol.186 , pp. 518-534
    • Klockgether, J.1    Reva, O.2    Larbig, K.3    Tümmler, B.4
  • 27
    • 0346997968 scopus 로고    scopus 로고
    • Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT
    • Böltner D, Osborn AM: Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT. Plasmid 2004, 51:12-23.
    • (2004) Plasmid , vol.51 , pp. 12-23
    • Böltner, D.1    Osborn, A.M.2
  • 28
    • 0032530804 scopus 로고    scopus 로고
    • The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O, 157:H7
    • Burland V, Shao Y, Perna NT, Plunkett G, Sofia HJ, Blattner FR: The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O, 157:H7. Nucleic Acids Res 1998, 26:4196-4204.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4196-4204
    • Burland, V.1    Shao, Y.2    Perna, N.T.3    Plunkett, G.4    Sofia, H.J.5    Blattner, F.R.6
  • 29
    • 0033817109 scopus 로고    scopus 로고
    • Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens
    • Hurst MRH, Glare TR, Jackson TA, Ronson CW: Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens. J Bacteriol 2000, 182:5127-5138.
    • (2000) J. Bacteriol. , vol.182 , pp. 5127-5138
    • Hurst, M.R.H.1    Glare, T.R.2    Jackson, T.A.3    Ronson, C.W.4
  • 30
    • 0345687907 scopus 로고    scopus 로고
    • The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state
    • Strömsten NJ, Benson SD, Burnett RM, Bamford DH, Bamford JKH: The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J Bacteriol 2003, 185:6985-6989.
    • (2003) J. Bacteriol. , vol.185 , pp. 6985-6989
    • Strömsten, N.J.1    Benson, S.D.2    Burnett, R.M.3    Bamford, D.H.4    Bamford, J.K.H.5
  • 31
    • 0032246556 scopus 로고    scopus 로고
    • Tailed bacteriophages: The order Caudovirales
    • Ackermann HW: Tailed bacteriophages: the order Caudovirales. Adv Virus Res 1998, 51:135-201.
    • (1998) Adv. Virus Res. , vol.51 , pp. 135-201
    • Ackermann, H.W.1
  • 33
    • 0038392706 scopus 로고    scopus 로고
    • Bacteriophage observations and evolution
    • Ackermann HW: Bacteriophage observations and evolution. Res Microbiol 2003, 154:245-251.
    • (2003) Res. Microbiol. , vol.154 , pp. 245-251
    • Ackermann, H.W.1
  • 35
    • 0344863179 scopus 로고    scopus 로고
    • The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1
    • Alonso JC, Luder G, Stiege AC, Chai S, Weise F, Trautner TA: The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 1997, 204: 01-212.
    • (1997) Gene , vol.204 , pp. 201-212
    • Alonso, J.C.1    Luder, G.2    Stiege, A.C.3    Chai, S.4    Weise, F.5    Trautner, T.A.6
  • 39
    • 0036937356 scopus 로고    scopus 로고
    • Global features of the Pseudomonas putida KT2440 genome sequence
    • Weinel C, Nelson KE, Tümmler B: Global features of the Pseudomonas putida KT2440 genome sequence. Envir Microbiol 2002, 4:809-818.
    • (2002) Envir. Microbiol. , vol.4 , pp. 809-818
    • Weinel, C.1    Nelson, K.E.2    Tümmler, B.3
  • 40
    • 10044246531 scopus 로고    scopus 로고
    • Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2, 440: Orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures
    • Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B: Comparative genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2, 440: orthologs, codon usage, repetitive extragenic palindromic elements, and oligonucleotide motif signatures. Genome Lett 2002, 1:175-187.
    • (2002) Genome Lett. , vol.1 , pp. 175-187
    • Weinel, C.1    Ussery, D.W.2    Ohlsson, H.3    Sicheritz-Ponten, T.4    Kiewitz, C.5    Tümmler, B.6
  • 41
    • 0036723852 scopus 로고    scopus 로고
    • R, 391: A conjugative integrating mosaic comprised of phage, plasmid, and transposon elements
    • Böltner D, MacMahon C, Pembroke JT, Strike P, Osborn AM: R, 391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J Bacteriol 2002, 184:5158-5169.
    • (2002) J. Bacteriol. , vol.184 , pp. 5158-5169
    • Böltner, D.1    MacMahon, C.2    Pembroke, J.T.3    Strike, P.4    Osborn, A.M.5
  • 43
    • 0038392697 scopus 로고    scopus 로고
    • Bacteriophages with tails: Chasing their origins and evolution
    • Hendrix RW, Hatfull GF, Smith MC: Bacteriophages with tails: chasing their origins and evolution. Res Microbiol 2003, 154:253-257.
    • (2003) Res. Microbiol. , vol.154 , pp. 253-257
    • Hendrix, R.W.1    Hatfull, G.F.2    Smith, M.C.3
  • 44
    • 0021109593 scopus 로고
    • A Markov analysis of DNA sequences
    • Almagor H: A Markov analysis of DNA sequences. J Theor Biol 1983, 104:633-645.
    • (1983) J. Theor. Biol. , vol.104 , pp. 633-645
    • Almagor, H.1
  • 45
    • 84874647903 scopus 로고    scopus 로고
    • Python home page
    • Python home page [http://www.python.org/]
  • 46
    • 84874658377 scopus 로고    scopus 로고
    • NCBI home page
    • NCBI home page [http://www.ncbi.nlm.nih.gov/]
  • 47
    • 84874666687 scopus 로고    scopus 로고
    • Plasmid genome database
    • Plasmid genome database [http://www.genomics.ceh.ac.uk/plasmiddb/]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.