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Volumn 11, Issue 6, 2004, Pages 361-370

Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1

Author keywords

Aeropyrum pernix K1; Gene recognition; Nucleotide composition; Protein coding genes; Three clusters

Indexed keywords

DNA;

EID: 21044451133     PISSN: 13402838     EISSN: None     Source Type: Journal    
DOI: 10.1093/dnares/11.6.361     Document Type: Article
Times cited : (16)

References (31)
  • 1
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin, M. Y. and Koonin, E. V. 1998, Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption, In Silica Biol., 1, 55-67.
    • (1998) In Silica Biol. , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 2
    • 0033616977 scopus 로고    scopus 로고
    • Complete genome sequence of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1
    • Kawarabayasi, Y., Hino, Y., Horikawa, H. et al. 1999, Complete genome sequence of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, DNA Res., 6, 83-101, 145-52.
    • (1999) DNA Res. , vol.6 , pp. 83-101
    • Kawarabayasi, Y.1    Hino, Y.2    Horikawa, H.3
  • 3
    • 0034572821 scopus 로고    scopus 로고
    • Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)
    • RESEARCH0009
    • Natale, D. A., Shankavaram, U. T., Galperin, M. Y., Wolf, Y. I., Aravind, L., and Koonin, E. V. 2000, Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs), Genome Biol., 1, RESEARCH0009.
    • (2000) Genome Biol. , vol.1
    • Natale, D.A.1    Shankavaram, U.T.2    Galperin, M.Y.3    Wolf, Y.I.4    Aravind, L.5    Koonin, E.V.6
  • 4
    • 2142859937 scopus 로고    scopus 로고
    • Reannotation of genome microbial coding-Sequences: Finding new genes and inaccurately annotated genes
    • Bocs, S., Danchin, A., and Medigue, C. 2002, Reannotation of genome microbial coding-Sequences: finding new genes and inaccurately annotated genes, BMC Bioinformatics, 3, 5.
    • (2002) BMC Bioinformatics , vol.3 , pp. 5
    • Bocs, S.1    Danchin, A.2    Medigue, C.3
  • 5
    • 0035424711 scopus 로고    scopus 로고
    • On the total number of genes and their length distribution in complete microbial genomes
    • Skovgaard, M., Jensen, L. J., Brunak, S., Ussery, D., and Krogh, A. 2001, On the total number of genes and their length distribution in complete microbial genomes, Trends Genet., 17, 425-428.
    • (2001) Trends Genet. , vol.17 , pp. 425-428
    • Skovgaard, M.1    Jensen, L.J.2    Brunak, S.3    Ussery, D.4    Krogh, A.5
  • 6
    • 0037251892 scopus 로고    scopus 로고
    • NCBI Reference Sequence project: Update and current status
    • Pruitt, K. D., Tatusova, T., and Maglott, D. R. 2003, NCBI Reference Sequence project: update and current status, Nucleic Acids Res., 31, 34-37.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 34-37
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 7
    • 0026059039 scopus 로고
    • Analysis of distribution of bases in the coding sequences by a diagrammatic technique
    • Zhang, C. T. and Zhang, R. 1991, Analysis of distribution of bases in the coding sequences by a diagrammatic technique, Nucleic Acids Res., 19, 6313-6317.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 6313-6317
    • Zhang, C.T.1    Zhang, R.2
  • 8
    • 0035162592 scopus 로고    scopus 로고
    • The COG database: New developments in phylogenetic classification of proteins from complete genomes
    • Tatusov, R. L., Natale, D. A., Garkavtsev, I. V. et al. 2001, The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Res., 29, 22-28.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 22-28
    • Tatusov, R.L.1    Natale, D.A.2    Garkavtsev, I.V.3
  • 10
    • 0036572274 scopus 로고    scopus 로고
    • Synonymous codon usage in Pseudomonas aeruginosa PA01
    • Grocock, R. J. and Sharp, P. M. 2002, Synonymous codon usage in Pseudomonas aeruginosa PA01, Gene, 289, 131-139.
    • (2002) Gene , vol.289 , pp. 131-139
    • Grocock, R.J.1    Sharp, P.M.2
  • 11
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • Garcia-Vallve, S., Romeu, A., and Palau, J. 2000, Horizontal gene transfer in bacterial and archaeal complete genomes, Genome Res., 10, 1719-1725.
    • (2000) Genome Res. , vol.10 , pp. 1719-1725
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 12
    • 0034888796 scopus 로고    scopus 로고
    • Ongoing evolution of strand composition in bacterial genomes
    • Rocha, E. P. and Danchin, A. 2001, Ongoing evolution of strand composition in bacterial genomes, Mol. Biol. Evol., 18, 1789-1799.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1789-1799
    • Rocha, E.P.1    Danchin, A.2
  • 13
    • 0032169578 scopus 로고    scopus 로고
    • Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
    • McInerney, J. O. 1998, Replicational and transcriptional selection on codon usage in Borrelia burgdorferi, Proc. Natl. Acad. Sci. USA., 95, 10698-10703.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 10698-10703
    • McInerney, J.O.1
  • 14
    • 0033118273 scopus 로고    scopus 로고
    • Proteome composition and codon usage in spirochaetes: Species-specific and DNA strand-specific mutational biases
    • Lafay, B., Lloyd, A. T., McLean, M. J., Devine, K. M., Sharp, P. M., and Wolfe, K. H. 1999, Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases, Nucleic Acids Res., 27, 1642-1649.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 1642-1649
    • Lafay, B.1    Lloyd, A.T.2    McLean, M.J.3    Devine, K.M.4    Sharp, P.M.5    Wolfe, K.H.6
  • 15
    • 0034657798 scopus 로고    scopus 로고
    • Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces
    • Romero, H., Zavala, A., and Musto, H. 2000, Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces, Nucleic Acids Res., 28, 2084-2090.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2084-2090
    • Romero, H.1    Zavala, A.2    Musto, H.3
  • 16
    • 84975862989 scopus 로고    scopus 로고
    • Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns
    • McInerney, J. O. 1997, Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns, Microb. Compar. Genomics, 2, 1-10.
    • (1997) Microb. Compar. Genomics , vol.2 , pp. 1-10
    • McInerney, J.O.1
  • 17
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence analysis in codon usage studies
    • Perriere, G. and Thioulouse, J. 2002, Use and misuse of correspondence analysis in codon usage studies, Nucleic Acids Res., 30, 4548-4555.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4548-4555
    • Perriere, G.1    Thioulouse, J.2
  • 18
    • 0037250391 scopus 로고    scopus 로고
    • HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
    • Garcia-Vallve, S., Guzman, E., Montero, M. A., and Romeu, A. 2003, HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes, Nucleic Acids Res., 31, 187-189.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 187-189
    • Garcia-Vallve, S.1    Guzman, E.2    Montero, M.A.3    Romeu, A.4
  • 19
    • 0023650543 scopus 로고
    • The codon Adaptation Index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M. and Li, W. H. 1987, The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Res., 15, 1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 20
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Mark models
    • Salzberg, S. L., Delcher, A. L., Kasif, S., and White, O. 1998, Microbial gene identification using interpolated Mark models, Nucleic Acids Res. 26, 544-548.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 544-548
    • Salzberg, S.L.1    Delcher, A.L.2    Kasif, S.3    White, O.4
  • 21
    • 0037716514 scopus 로고    scopus 로고
    • Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages
    • Chen, L. L. and Zhang, C. T. 2003, Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages, Biochem. Biophys. Res. Commun., 306, 310-317.
    • (2003) Biochem. Biophys. Res. Commun. , vol.306 , pp. 310-317
    • Chen, L.L.1    Zhang, C.T.2
  • 22
    • 1842423288 scopus 로고    scopus 로고
    • Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney
    • Nakagawa, S., Takai, K., Horikoshi, K., and Sako, Y. 2004, Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int. J. Syst. Evol. Microbiol., 54, 329-335.
    • (2004) Int. J. Syst. Evol. Microbiol. , vol.54 , pp. 329-335
    • Nakagawa, S.1    Takai, K.2    Horikoshi, K.3    Sako, Y.4
  • 23
    • 0037444091 scopus 로고    scopus 로고
    • ZCURVE: A new system for recognizing protein-coding genes in bacterial and archaeal genomes
    • Guo, F. B., Ou, H. Y., and Zhang, C. T. 2003, ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes, Nucleic Acids Res., 31, 1780-1789.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1780-1789
    • Guo, F.B.1    Ou, H.Y.2    Zhang, C.T.3
  • 24
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira, A., Ochman, H., and Moran, N. A. 2001, Deletional bias and the evolution of bacterial genomes, Trends Genet., 17, 589-596.
    • (2001) Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 25
    • 0031911710 scopus 로고    scopus 로고
    • The role of the genetic code in generating new coding sequences inside existing genes
    • Cebrat, S., Mackiewicz, P., and Dudek, M. R. 1998, The role of the genetic code in generating new coding sequences inside existing genes, Biosystems, 45, 165-176.
    • (1998) Biosystems , vol.45 , pp. 165-176
    • Cebrat, S.1    Mackiewicz, P.2    Dudek, M.R.3
  • 26
    • 0017298367 scopus 로고
    • Overlapping genes in bacteriophage phiX174
    • Barrell, B. G., Air, G. M., and Hutchison, C. A. 3rd. 1976, Overlapping genes in bacteriophage phiX174, Nature, 264, 34-41.
    • (1976) Nature , vol.264 , pp. 34-41
    • Barrell, B.G.1    Air, G.M.2    Hutchison III, C.A.3
  • 27
    • 0037431063 scopus 로고    scopus 로고
    • Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3 (2) using the Z curve method
    • Ou, H. Y., Guo, F. B., and Zhang, C. T. 2003, Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3 (2) using the Z curve method, FEBS Lett., 540, 188-194.
    • (2003) FEBS Lett. , vol.540 , pp. 188-194
    • Ou, H.Y.1    Guo, F.B.2    Zhang, C.T.3
  • 28
    • 0842346757 scopus 로고    scopus 로고
    • Seven clusters in genomic triplet distributions
    • Gorban, A. N., Zinovyev, A. Y., and Popova, T. G. 2003, Seven clusters in genomic triplet distributions, In silica Biol., 3, 471-482.
    • (2003) In Silica Biol. , vol.3 , pp. 471-482
    • Gorban, A.N.1    Zinovyev, A.Y.2    Popova, T.G.3
  • 29
    • 0028237028 scopus 로고
    • A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences
    • Zhang, C. T. and Chou, K. C. 1995, A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences, J. Mol. Biol., 238, 1-8.
    • (1995) J. Mol. Biol. , vol.238 , pp. 1-8
    • Zhang, C.T.1    Chou, K.C.2
  • 30
    • 0023194889 scopus 로고
    • Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences
    • Trifonov, E. N. 1987, Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences, J. Mol. Biol., 194, 643-652.
    • (1987) J. Mol. Biol. , vol.194 , pp. 643-652
    • Trifonov, E.N.1
  • 31
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset, M. and Guigo, R. 1996, Evaluation of gene structure prediction programs, Genomics, 34, 353-357.
    • (1996) Genomics , vol.34 , pp. 353-357
    • Burset, M.1    Guigo, R.2


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