메뉴 건너뛰기




Volumn 15, Issue 11, 1999, Pages 874-886

Finding prokaryotic genes by the 'frame-by-frame' algorithm: Targeting gene starts and overlapping genes

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; COMPUTER PROGRAM; CONFERENCE PAPER; DNA SEQUENCE; GENE; GENE STRUCTURE; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROBABILITY; PROKARYOTE; START CODON; TRANSLATION INITIATION;

EID: 0033384536     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.11.874     Document Type: Conference Paper
Times cited : (40)

References (32)
  • 3
    • 0000241874 scopus 로고
    • GeneMark: Parallel gene recognition for both DNA strands
    • Borodovsky, M. and McIninch, J.D. (1993) GeneMark: parallel gene recognition for both DNA strands. Comput. Chem., 17, 123-133.
    • (1993) Comput. Chem. , vol.17 , pp. 123-133
    • Borodovsky, M.1    McIninch, J.D.2
  • 4
    • 0029056051 scopus 로고
    • Detection of new genes in the bacterial genome using markov models for three gene classes
    • Borodovsky, M., McIninch, J., Koonin, E., Rudd, K., Medigue, C. and Danchin, A. (1995) Detection of new genes in the bacterial genome using markov models for three gene classes. Nucleic Acids Res., 23, 3554-3562.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3554-3562
    • Borodovsky, M.1    McIninch, J.2    Koonin, E.3    Rudd, K.4    Medigue, C.5    Danchin, A.6
  • 5
    • 0005817683 scopus 로고    scopus 로고
    • Statistical predictions of coding regions in prokaryotic genomes by using inhomogeneous Markov models
    • Charlebois, R. (ed). ASM Press, Washington, DC
    • Borodovsky, M., Hayes, W.S. and Lukashin, A. (1999) Statistical predictions of coding regions in prokaryotic genomes by using inhomogeneous Markov models. In Charlebois, R. (ed). The Organization of the Prokaryotic Genome. ASM Press, Washington, DC, pp. 11-13.
    • (1999) The Organization of the Prokaryotic Genome , pp. 11-13
    • Borodovsky, M.1    Hayes, W.S.2    Lukashin, A.3
  • 6
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archeon, Methanococcus jannaschii
    • Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G. et al. (1996) Complete genome sequence of the methanogenic archeon, Methanococcus jannaschii. Science, 273, 1058-1073.
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bult, C.J.1    White, O.2    Olsen, G.J.3    Zhou, L.4    Fleischmann, R.D.5    Sutton, G.G.6
  • 7
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 8
    • 0032508046 scopus 로고    scopus 로고
    • Deciphering the bacteriology of Microbacterium tuberculosis from the complete genome sequence
    • Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V. et al. (1998) Deciphering the bacteriology of Microbacterium tuberculosis from the complete genome sequence. Nature, 393, 537-544.
    • (1998) Nature , vol.393 , pp. 537-544
    • Cole, S.T.1    Brosch, R.2    Parkhill, J.3    Garnier, T.4    Churcher, C.5    Harris, D.6    Gordon, S.V.7
  • 9
    • 0020480512 scopus 로고
    • Recognition of protein-coding regions in DNA sequences
    • Fickett, J. (1982) Recognition of protein-coding regions in DNA sequences. Nucleic Acids Res., 10, 5303-5318.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 5303-5318
    • Fickett, J.1
  • 11
    • 0015600423 scopus 로고
    • The Viterbi Algorithm
    • Forney, G.D. (1973) The Viterbi Algorithm. IEEE Proceedings, 61, 268-278.
    • (1973) IEEE Proceedings , vol.61 , pp. 268-278
    • Forney, G.D.1
  • 13
    • 0032526322 scopus 로고    scopus 로고
    • Combining diverse evidence for gene recognition in completely sequenced bacterial genomes
    • Erratum in Nucleic Acids Res., 26, 3870
    • Frishman, D., Mironov, A., Mewes, H.-W. and Gelfand, M. (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res., 26, 2941-2947. (Erratum in Nucleic Acids Res., 26, 3870).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2941-2947
    • Frishman, D.1    Mironov, A.2    Mewes, H.-W.3    Gelfand, M.4
  • 14
    • 0021760027 scopus 로고
    • The codon preference plot: Graphic analysis of protein coding sequences and prediction of gene expression
    • Gribskov, M., Devereux, J. and Burgess, R.R. (1984) The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res., 12, 539-549.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 539-549
    • Gribskov, M.1    Devereux, J.2    Burgess, R.R.3
  • 16
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different classes of the Escherichia coli genome
    • Karlin, S., Mrazek, J. and Campbell, A. (1998) Codon usages in different classes of the Escherichia coli genome. Mol. Microbiol., 29, 1341-1355.
    • (1998) Mol. Microbiol. , vol.29 , pp. 1341-1355
    • Karlin, S.1    Mrazek, J.2    Campbell, A.3
  • 17
    • 0030606607 scopus 로고    scopus 로고
    • Sequence analysis of the genome of the unicellular cyanobacterium Synechosistis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions
    • Kaneko, K., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y. et al. (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechosistis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res., 3, 109-136.
    • (1996) DNA Res. , vol.3 , pp. 109-136
    • Kaneko, K.1    Sato, S.2    Kotani, H.3    Tanaka, A.4    Asamizu, E.5    Nakamura, Y.6
  • 19
    • 0031458333 scopus 로고    scopus 로고
    • The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeglobus fulgidus
    • Klenk, H.P., Clayton, R.A., Torab, J.F., White, O., Nelson, K.E., Ketchum, K.A. et al. (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeglobus fulgidus. Nature, 390, 364-370.
    • (1997) Nature , vol.390 , pp. 364-370
    • Klenk, H.P.1    Clayton, R.A.2    Torab, J.F.3    White, O.4    Nelson, K.E.5    Ketchum, K.A.6
  • 20
    • 0027944605 scopus 로고
    • A hidden Markov model that finds genes in E.coli DNA
    • Krogh, A., Mian, I.S. and Haussler, D. (1994) A hidden Markov model that finds genes in E.coli DNA. Nucleic Acids Res., 22, 4768-4778.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4768-4778
    • Krogh, A.1    Mian, I.S.2    Haussler, D.3
  • 21
    • 0030731108 scopus 로고    scopus 로고
    • The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
    • Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Science, 390, 249-256.
    • (1997) Science , vol.390 , pp. 249-256
    • Kunst, F.1    Ogasawara, N.2    Moszer, I.3    Albertini, A.M.4    Alloni, G.5    Azevedo, V.6
  • 22
    • 0030805979 scopus 로고    scopus 로고
    • Comparing the predicted and observed properties of proteins encoded in the geneome of Escherichia coli K-12
    • Link, A.J., Robison, K. and Church, G.M. (1997) Comparing the predicted and observed properties of proteins encoded in the geneome of Escherichia coli K-12. Electrophoresis, 18, 1259-1313.
    • (1997) Electrophoresis , vol.18 , pp. 1259-1313
    • Link, A.J.1    Robison, K.2    Church, G.M.3
  • 23
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 26, 1107-1115.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 24
    • 0026332291 scopus 로고
    • Evidence for horizontal gene transfer in Escherichia coli speciation
    • Medigue, C., Rouxel, T., Vigien, A., Henaut, A. and Danchin, A. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222, 851-856.
    • (1991) J. Mol. Biol. , vol.222 , pp. 851-856
    • Medigue, C.1    Rouxel, T.2    Vigien, A.3    Henaut, A.4    Danchin, A.5
  • 25
    • 0028291320 scopus 로고
    • Large-scale bacterial gene discovery by similarity search
    • Robison, K., Gilbert, W. and Church, G. (1994) Large-scale bacterial gene discovery by similarity search. Nat. Genet., 7, 205-214.
    • (1994) Nat. Genet. , vol.7 , pp. 205-214
    • Robison, K.1    Gilbert, W.2    Church, G.3
  • 26
    • 15644383855 scopus 로고    scopus 로고
    • Complete genome sequence of Methanobacterium thermoautotrophicum delta H: Functional analysis and comparative genomics
    • Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H.-M., Dubois, J., Aldredge, T. et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum delta H: functional analysis and comparative genomics. J. Bacteriol., 179, 7135-7155.
    • (1997) J. Bacteriol. , vol.179 , pp. 7135-7155
    • Smith, D.R.1    Doucette-Stamm, L.A.2    Deloughery, C.3    Lee, H.-M.4    Dubois, J.5    Aldredge, T.6
  • 27
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • Salzberg, S.L., Delcher, A.L., Kasif, S. and White, O. (1998) Microbial gene identification using interpolated Markov 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
  • 28
    • 0021760028 scopus 로고
    • Measurements of the effect that coding for a protein has on DNA sequence and their use for finding genes
    • Staden, R. (1984) Measurements of the effect that coding for a protein has on DNA sequence and their use for finding genes. Nucleic Acids Res., 12, 551-567.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 551-567
    • Staden, R.1
  • 29
    • 12944316109 scopus 로고    scopus 로고
    • The construction of the mathematical model of DNA in the form of uniform Markov chain and the possibility of its usage for gene recognition
    • in press
    • Smatkov, A.M. (1999) The construction of the mathematical model of DNA in the form of uniform Markov chain and the possibility of its usage for gene recognition (in Russian). Izvestia RAS, The Theory and Control Systems, (in press).
    • (1999) Izvestia RAS, the Theory and Control Systems
    • Smatkov, A.M.1
  • 31
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Viterbi, A.J. (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Informat. Theory, V, IT-13, 260-269.
    • (1967) IEEE Trans. Informat. Theory, V , vol.IT-13 , pp. 260-269
    • Viterbi, A.J.1
  • 32
    • 0028605559 scopus 로고
    • Constructing gene models from accurately predicted exons: An application of dynamic programming
    • Xu, Y., Einstein, J.R., Mural, R.J., Shah, M. and Uberbacher, E.C. (1994) Constructing gene models from accurately predicted exons: an application of dynamic programming. Comput. Appl. Biosci., 10, 613-623.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 613-623
    • Xu, Y.1    Einstein, J.R.2    Mural, R.J.3    Shah, M.4    Uberbacher, E.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.