메뉴 건너뛰기




Volumn 2, Issue 2, 2004, Pages 353-373

Multivariate entropy distance method for prokaryotic gene identification

Author keywords

Entropy; Gene finding algorithm; Linguistic description of DNA

Indexed keywords

AMINO ACID; DNA; RNA;

EID: 4043165754     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000624     Document Type: Article
Times cited : (19)

References (39)
  • 1
    • 0000377189 scopus 로고    scopus 로고
    • "The gene identification problem: An overview for developers"
    • J. W. Fickett. "The gene identification problem: An overview for developers". Comput. Chem. 20, 103-118 (1996).
    • (1996) Comput. Chem. , vol.20 , pp. 103-118
    • Fickett, J.W.1
  • 2
    • 0036733640 scopus 로고    scopus 로고
    • "Computational prediction of eukaryotic protein coding genes"
    • M. Q. Zhang. "Computational prediction of eukaryotic protein coding genes". Nat. Rev. Genet. 3, 698-709 (2002).
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 698-709
    • Zhang, M.Q.1
  • 3
    • 0037096851 scopus 로고    scopus 로고
    • "Dictionary-driven prokaryotic gene finding"
    • T. Shibuya and I. Rigoutsos. "Dictionary-driven prokaryotic gene finding". Nucleic Acids Res. 30, 2710-2725 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2710-2725
    • Shibuya, T.1    Rigoutsos, I.2
  • 4
    • 0000241874 scopus 로고
    • "GENMARK: Parallel gene recognition for both DNA strands"
    • M. Borodovsky and J. McIninch. "GENMARK: parallel gene recognition for both DNA strands". Comput. Chem. 17, 123-134 (1993).
    • (1993) Comput. Chem. , vol.17 , pp. 123-134
    • Borodovsky, M.1    McIninch, J.2
  • 5
    • 0032519353 scopus 로고    scopus 로고
    • "GeneMark.hmm: New solutions for gene finding"
    • A. V. Lukashin and M. Borodovsky. "GeneMark.hmm: new solutions for gene finding". Nucleic Acids Res. 26, 1107-1115 (1998 ).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 6
    • 0035875343 scopus 로고    scopus 로고
    • "GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions"
    • J. Besemer, A. Lomsadze and M. Borodovsky. "GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. lmplications for finding sequence motifs in regulatory regions". Nucleic Acids Res. 29, 2607 2618 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2607-2618
    • Besemer, J.1    Lomsadze, A.2    Borodovsky, M.3
  • 7
    • 0032518163 scopus 로고    scopus 로고
    • "Microbial gene identification using interpolated Markov models"
    • S. L. Salzberg, A. L. Delcher, S. Kasif and O. White. "Microbial gene identification using interpolated Markov models". Nucleic Acids Res. 26, 544-548 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 544-548
    • Salzberg, S.L.1    Delcher, A.L.2    Kasif, S.3    White, O.4
  • 10
    • 0020480512 scopus 로고
    • "Recognition of protein coding regions in DNA sequences"
    • J. W. Fichett. "Recognition of protein coding regions in DNA sequences". Nucleic Acids Res. 10, 5303-5318 (1982).
    • (1982) Nucleic Acids Res. , vol.10 , pp. 5303-5318
    • Fichett, J.W.1
  • 11
    • 0023664981 scopus 로고
    • "Periodicities in introns"
    • P. G. Arqus and C. J. Michel. "Periodicities in introns". Nucleic Acids Res. 15, 7581-7592 (1987).
    • (1987) Nucleic Acids Res. , vol.15 , pp. 7581-7592
    • Arqus, P.G.1    Michel, C.J.2
  • 12
    • 0013630297 scopus 로고    scopus 로고
    • "Nested retrotransposons in the intergenic regions of the maize genome"
    • P. SanMiguel, et al. "Nested retrotransposons in the intergenic regions of the maize genome". Science 274, 765-768 (1996 ).
    • (1996) Science , vol.274 , pp. 765-768
    • SanMiguel, P.1
  • 13
    • 0031298464 scopus 로고    scopus 로고
    • "The study of correlation structures of DNA sequences: A critical review"
    • W. Li. "The study of correlation structures of DNA sequences: a critical review". Comput. Chem. 21, 257-271 (1997).
    • (1997) Comput. Chem. , vol.21 , pp. 257-271
    • Li, W.1
  • 14
    • 0027059264 scopus 로고
    • "Assessment of protein coding measures"
    • J. W. Fickett and C.-S. Tung. "Assessment of protein coding measures". Nucleic Acids Res. 20, 6441-6450 (1992).
    • (1992) Nucleic Acids Res. , vol.20 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.-S.2
  • 15
    • 0033214628 scopus 로고    scopus 로고
    • "Heuristic approach to deriving models for gene finding"
    • J. Besemer and M. Borodovsky. "Heuristic approach to deriving models for gene finding". Nucleic Acids Res. 27, 3911-3920 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 16
    • 0026059039 scopus 로고
    • "Analysis of distribution of bases in the coding sequences by a diagrammatic technique"
    • C.-T. Zhang and R. Zhang. "Analysis of distribution of bases in the coding sequences by a diagrammatic technique". Nucleic Acids Res. 19, 6313-6317 (1991).
    • (1991) Nucleic Acids Res. , vol.19 , pp. 6313-6317
    • Zhang, C.-T.1    Zhang, R.2
  • 17
    • 0037444091 scopus 로고    scopus 로고
    • "ZCURVE: A new system 1for recognizing protein-coding genes in bacterial and archaeal lgenomes"
    • F.-B. Guo, H.-Y. On and C.-T. Zhang. "ZCURVE: a new system 1for recognizing protein-coding genes in bacterial and archaeal lgenomes". Nucleic Acids Res. 31, 1780-1789 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1780-1789
    • Guo, F.-B.1    On, H.-Y.2    Zhang, C.-T.3
  • 18
    • 84856043672 scopus 로고
    • "A mathematical theory of communication"
    • 379-423 and
    • C. E. Shannon. "A mathematical theory of communication". Bell System Technical Journal 27, 379-423 and 623-656 (1948).
    • (1948) Bell System Technical Journal , vol.27 , pp. 623-656
    • Shannon, C.E.1
  • 19
    • 0037251892 scopus 로고    scopus 로고
    • "RefSeq and LocusLink: NCBI gene-centered resources"
    • K. Pruitt, T. Tatusov and D. Maglott. "RefSeq and LocusLink: NCBI gene-centered resources". Nucleic Acid Res. 31, 34-37 (2003).
    • (2003) Nucleic Acid Res. , vol.31 , pp. 34-37
    • Pruitt, K.1    Tatusov, T.2    Maglott, D.3
  • 25
    • 0030606607 scopus 로고    scopus 로고
    • "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions"
    • T. Kaneko, S. Sato, H. Kotani, A. Tanaka, E. Asarnizu, Y. Nakamura, N. Miyajima, M. Hirosawa, M. Súgiura, S. Sasamoto, et al. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions". DNA Res. 3, 109-136 (1996).
    • (1996) DNA Res. , vol.3 , pp. 109-136
    • Kaneko, T.1    Sato, S.2    Kotani, H.3    Tanaka, A.4    Asarnizu, E.5    Nakamura, Y.6    Miyajima, N.7    Hirosawa, M.8    Súgiura, M.9    Sasamoto, S.10
  • 30
    • 0019858614 scopus 로고
    • "Similar amino acid sequences: Chance or common ancestry?"
    • R. F. Doolittle. "Similar amino acid sequences: chance or common ancestry?" Science 214, 149-159 (1981).
    • (1981) Science , vol.214 , pp. 149-159
    • Doolittle, R.F.1
  • 31
    • 0027279050 scopus 로고
    • "Rapid identification of proteins"
    • G. Shaw. "Rapid identification of proteins". Proc. Natl. Acad. Sci. 90, 5138-5142 (1993).
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 5138-5142
    • Shaw, G.1
  • 32
    • 0029115481 scopus 로고
    • "A sequence property approach to searching protein databases"
    • U. Hobohm and C. Sander. "A sequence property approach to searching protein databases". J. Mol. Biol. 251, 390-399 (1995).
    • (1995) J. Mol. Biol. , vol.251 , pp. 390-399
    • Hobohm, U.1    Sander, C.2
  • 33
    • 0030585734 scopus 로고    scopus 로고
    • "Evaluation of gene structure prediction programs"
    • M. Burset and R. Guigó. "Evaluation of gene structure prediction programs". Genomics 34, 353-367 (1996).
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigó, R.2
  • 34
    • 0030805979 scopus 로고    scopus 로고
    • "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12"
    • A. J. Link, K. Robison and G. M. Church. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12". Electrophoresis 18, 1259-1313 (1997).
    • (1997) Electrophoresis , vol.18 , pp. 1259-1313
    • Link, A.J.1    Robison, K.2    Church, G.M.3
  • 35
    • 0037306453 scopus 로고    scopus 로고
    • "Ancient horizontal gene transfer"
    • J. R. Brown. "Ancient horizontal gene transfer". Nat Rev Genet. 4, 121-132 (2003).
    • (2003) Nat Rev Genet. , vol.4 , pp. 121-132
    • Brown, J.R.1
  • 37
    • 0035424599 scopus 로고    scopus 로고
    • "Intrinsic errors in genome annotation"
    • D. Devos and A. Valencia. "Intrinsic errors in genome annotation". Trends Genet. 17, 429-431 (2001).
    • (2001) Trends Genet. , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 38
    • 2142859937 scopus 로고    scopus 로고
    • "Re-annotation of genome microbial CoDing-Sequencing: Finding new genes and inaccurately annotated genes"
    • S. Bocs, A. Danchin and C. Medigue. "Re-annotation of genome microbial CoDing-Sequencing: finding new genes and inaccurately annotated genes". BMC Bioinformatics 3, 5 (2002).
    • (2002) BMC Bioinformatics , vol.3 , pp. 5
    • Bocs, S.1    Danchin, A.2    Medigue, C.3
  • 39
    • 0005210357 scopus 로고    scopus 로고
    • (in Chinese) Shanghai Scientific and Technological Press, Shanghai, China
    • B. L. Hao, and S. Y. Zhang. A Handbook on Bioinformatics. (in Chinese), Shanghai Scientific and Technological Press, Shanghai, China. Pp. 183-184 (2000).
    • (2000) A Handbook on Bioinformatics , pp. 183-184
    • Hao, B.L.1    Zhang, S.Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.