메뉴 건너뛰기




Volumn 226, Issue 1, 1999, Pages 129-137

Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences

Author keywords

Functional signal; Gene detection; Local alignment; Mismatch; Synonymous codon

Indexed keywords

PROTEIN;

EID: 0033534799     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(98)00509-5     Document Type: Article
Times cited : (16)

References (34)
  • 2
    • 0024805395 scopus 로고
    • The isochore organization of the human genome
    • Bernardi G. The isochore organization of the human genome. Annu. Rev. Genet. 23:1989;637-661.
    • (1989) Annu. Rev. Genet. , vol.23 , pp. 637-661
    • Bernardi, G.1
  • 3
    • 0000241874 scopus 로고
    • GenMark: Parallel gene recognition for both DNA strands
    • Borodovsky M., McIninch J. GenMark: Parallel gene recognition for both DNA strands. Comput. Chem. 17:1993;123-133.
    • (1993) Comput. Chem. , vol.17 , pp. 123-133
    • Borodovsky, M.1    McIninch, J.2
  • 4
    • 0027940025 scopus 로고
    • New genes in old sequences: Strategy for finding genes in the bacterial genome
    • Borodovsky M., Koonin E.V., Rudd K.E. New genes in old sequences: Strategy for finding genes in the bacterial genome. Trends Biochem. Sci. 19:1994;309-313.
    • (1994) Trends Biochem. Sci. , vol.19 , pp. 309-313
    • Borodovsky, M.1    Koonin, E.V.2    Rudd, K.E.3
  • 5
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structure in human genomic DNA
    • Burge C., Karlin S. Prediction of complete gene structure in human genomic DNA. J. Mol. Biol. 268:1997;78-94.
    • (1997) J. Mol. Biol. , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 6
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction program
    • Burset M., Guigo R. Evaluation of gene structure prediction program. Genomics. 34:1996;353-367.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigo, R.2
  • 7
    • 0027944162 scopus 로고
    • Gene structure prediction by linguistic methods
    • Dong S., Searls D.B. Gene structure prediction by linguistic methods. Genomics. 23:1994;540-551.
    • (1994) Genomics , vol.23 , pp. 540-551
    • Dong, S.1    Searls, D.B.2
  • 8
    • 0029894792 scopus 로고    scopus 로고
    • The yeast genome project: What did we learn?
    • Dujon B. The yeast genome project: what did we learn? Trends Genet. 12:1996;263-270.
    • (1996) Trends Genet. , vol.12 , pp. 263-270
    • Dujon, B.1
  • 9
    • 0030218799 scopus 로고    scopus 로고
    • Finding genes by computer: The state of the art
    • Fickett J.W. Finding genes by computer: the state of the art. Trends Genet. 12:1996;316-320.
    • (1996) Trends Genet. , vol.12 , pp. 316-320
    • Fickett, J.W.1
  • 10
    • 0025040574 scopus 로고
    • GM: A practical tool for automating DNA sequence analysis
    • Fields C.A., Soderlund C.A. GM: a practical tool for automating DNA sequence analysis. Comput. Appl. Biosci. 6:1990;263-270.
    • (1990) Comput. Appl. Biosci. , vol.6 , pp. 263-270
    • Fields, C.A.1    Soderlund, C.A.2
  • 11
    • 0025000924 scopus 로고
    • Computer prediction of the exon-intron structure of mammalian pre-mRNAs
    • Gelfand M.S. Computer prediction of the exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Res. 18:1990;5865-5869.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 5865-5869
    • Gelfand, M.S.1
  • 12
    • 0029258948 scopus 로고
    • Prediction of function in DNA sequence analysis
    • Gelfand M.S. Prediction of function in DNA sequence analysis. J. Comput. Biol. 1:1995;87-115.
    • (1995) J. Comput. Biol. , vol.1 , pp. 87-115
    • Gelfand, M.S.1
  • 14
    • 0027399530 scopus 로고
    • Identification of protein coding regions by database similarity search
    • Gish W., States D.J. Identification of protein coding regions by database similarity search. Nature Genet. 3:1993;266-272.
    • (1993) Nature Genet. , vol.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 16
    • 0345220765 scopus 로고    scopus 로고
    • Finding genes in human DNA with a hidden Markov Model
    • Henderson J., Salzberg S., Fasman K. Finding genes in human DNA with a hidden Markov Model. J. Comp. Biol. 4:1997;119-126.
    • (1997) J. Comp. Biol. , vol.4 , pp. 119-126
    • Henderson, J.1    Salzberg, S.2    Fasman, K.3
  • 17
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89:1992;10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 18
    • 0026623434 scopus 로고
    • The prediction of exons through an analysis of spliceable open reading frames
    • Hutchinson G.B., Hayden M.R. The prediction of exons through an analysis of spliceable open reading frames. Nucleic Acids Res. 20:1992;3453-3462.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 3453-3462
    • Hutchinson, G.B.1    Hayden, M.R.2
  • 19
    • 0030094146 scopus 로고    scopus 로고
    • CENSOR - A program for identification and elimination of repetitive elements from DNA sequences
    • Jurka J., Klonowski P., Dagman V., Pelton P. CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20:1996;119-122.
    • (1996) Comput. Chem. , vol.20 , pp. 119-122
    • Jurka, J.1    Klonowski, P.2    Dagman, V.3    Pelton, P.4
  • 20
    • 0030333286 scopus 로고    scopus 로고
    • A generalized hidden Markov model for the recognition of human genes in DNA
    • In: States, D.J., Agarwal, P., Gaasterland, T., Hunter, L., Smith, R. (Eds.), AAAI Press, Menlo Park
    • Kulp, D., Haussler, D., Reese, M.G., Eeckman, F.H., 1996. A generalized hidden Markov model for the recognition of human genes in DNA. In: States, D.J., Agarwal, P., Gaasterland, T., Hunter, L., Smith, R. (Eds.), Proc. 4th Int. Conf. Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, pp. 134-142.
    • (1996) Proc. 4th Int. Conf. Intelligent Systems for Molecular Biology , pp. 134-142
    • Kulp, D.1    Haussler, D.2    Reese, M.G.3    Eeckman, F.H.4
  • 23
    • 0002276095 scopus 로고    scopus 로고
    • Prediction of human gene structure
    • In: Bishop, M.J. (Ed.), Academic Press, London
    • Milanesi, L., Rogozin, I.B., 1998. Prediction of human gene structure. In: Bishop, M.J. (Ed.), Guide to Human Genome Computing. Academic Press, London, pp. 215-259.
    • (1998) Guide to Human Genome Computing , pp. 215-259
    • Milanesi, L.1    Rogozin, I.B.2
  • 24
    • 0025936264 scopus 로고
    • Multigene families and the evolution of complexity
    • Ohta T. Multigene families and the evolution of complexity. J. Mol. Evol. 33:1991;34-41.
    • (1991) J. Mol. Evol. , vol.33 , pp. 34-41
    • Ohta, T.1
  • 25
    • 0025726597 scopus 로고
    • Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection
    • Rogozin I.B., Solovyev V.V., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes. I. Correlation between somatic mutations and repeats. Somatic mutation properties and clonal selection. Biochim. Biophys. Acta. 1089:1991;175-182.
    • (1991) Biochim. Biophys. Acta , vol.1089 , pp. 175-182
    • Rogozin, I.B.1    Solovyev, V.V.2    Kolchanov, N.A.3
  • 26
    • 0029955046 scopus 로고    scopus 로고
    • Gene structure prediction using information on homologous protein sequence
    • Rogozin I.B., Milanesi L., Kolchanov N.A. Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci. 12:1996;161-170.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 161-170
    • Rogozin, I.B.1    Milanesi, L.2    Kolchanov, N.A.3
  • 27
    • 0030787856 scopus 로고    scopus 로고
    • Analysis of donor splice sites in different eukaryotic organisms
    • Rogozin I.B., Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. J. Mol. Evol. 45:1997;50-59.
    • (1997) J. Mol. Evol. , vol.45 , pp. 50-59
    • Rogozin, I.B.1    Milanesi, L.2
  • 28
    • 0025321246 scopus 로고
    • Splice junctions, branch point sites, and exons: Sequence statistics, identification and Genome Project
    • Senapathy P., Shapiro M.B., Harris N.L. Splice junctions, branch point sites, and exons: sequence statistics, identification and Genome Project. Meth. Enzymol. 183:1990;252-278.
    • (1990) Meth. Enzymol. , vol.183 , pp. 252-278
    • Senapathy, P.1    Shapiro, M.B.2    Harris, N.L.3
  • 29
    • 0027229632 scopus 로고
    • Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural networks
    • Snyder E.E., Stormo G.D. Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res. 21:1993;607-613.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 607-613
    • Snyder, E.E.1    Stormo, G.D.2
  • 30
    • 0028618270 scopus 로고
    • Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames
    • Solovyev V.V., Salamov A.A., Lawrence C.B. Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22:1994;5156-5163.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5156-5163
    • Solovyev, V.V.1    Salamov, A.A.2    Lawrence, C.B.3
  • 31
    • 0028401927 scopus 로고
    • Combined use of sequence similarity and codon bias for coding region identification
    • States D.J., Gish W. Combined use of sequence similarity and codon bias for coding region identification. J. Comput. Biol. 1:1994;39-50.
    • (1994) J. Comput. Biol. , vol.1 , pp. 39-50
    • States, D.J.1    Gish, W.2
  • 32
    • 77957187566 scopus 로고
    • A probabilistic model for detecting coding regions in DNA sequences
    • Thomas A., Skolnick M.H. A probabilistic model for detecting coding regions in DNA sequences. IMA J. Math. Appl. Med. Biol. 11:1994;149-160.
    • (1994) IMA J. Math. Appl. Med. Biol. , vol.11 , pp. 149-160
    • Thomas, A.1    Skolnick, M.H.2
  • 33
    • 0026351408 scopus 로고
    • Locating protein coding segments in human DNA sequences by a multiple sensor-neural network approach
    • Uberbacher E.C., Mural R.J. Locating protein coding segments in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA. 88:1991;11261-11265.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 11261-11265
    • Uberbacher, E.C.1    Mural, R.J.2
  • 34
    • 0031027525 scopus 로고    scopus 로고
    • Identification of protein coding regions in the human genome based on quadratic discriminant analysis
    • Zhang M.Q. Identification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. USA. 94:1997;565-568.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 565-568
    • Zhang, M.Q.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.