메뉴 건너뛰기




Volumn 30, Issue 19, 2002, Pages 4103-4117

Current methods of gene prediction, their strengths and weaknesses

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARABIDOPSIS; COMPUTER PROGRAM; CONTROLLED STUDY; EUKARYOTE; EXPRESSED SEQUENCE TAG; GENE LOCATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENOME; HUMAN; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE DATABASE;

EID: 0036796369     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf543     Document Type: Review
Times cited : (347)

References (156)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • The International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome
    • The International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 2
    • 0034649566 scopus 로고    scopus 로고
    • The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 5
    • 0031298796 scopus 로고    scopus 로고
    • The difficulty of identifying genes in anonymous vertebrate sequences
    • Claverie,J.M., Poirot,O. and Lopez,F. (1997) The difficulty of identifying genes in anonymous vertebrate sequences. Comput. Chem., 21, 203-214.
    • (1997) Comput. Chem , vol.21 , pp. 203-214
    • Claverie, J.M.1    Poirot, O.2    Lopez, F.3
  • 6
    • 0035313211 scopus 로고    scopus 로고
    • Computational methods for gene annotation: The Arabidopsis genome
    • Cho,Y. and Walbot,V. (2001) Computational methods for gene annotation: the Arabidopsis genome. Curr. Opin. Biotechnol., 12, 126-130.
    • (2001) Curr. Opin. Biotechnol , vol.12 , pp. 126-130
    • Cho, Y.1    Walbot, V.2
  • 7
    • 0028004414 scopus 로고
    • Intrinsic and and extrinsic approached for detecting genes in a bacterial genome
    • Borodovsky,M., Rudd,K.E. and Koonin,E.V. (1994) Intrinsic and and extrinsic approached for detecting genes in a bacterial genome. Nucleic Acids Res., 22, 4756-4767.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4756-4767
    • Borodovsky, M.1    Rudd, K.E.2    Koonin, E.V.3
  • 8
    • 0000377189 scopus 로고    scopus 로고
    • The gene identification problem: An overview for developer
    • Fickett,J.W. (1996) The gene identification problem: an overview for developer. Comput. Chem., 20, 103-118.
    • (1996) Comput. Chem , vol.20 , pp. 103-118
    • Fickett, J.W.1
  • 9
    • 0033118642 scopus 로고    scopus 로고
    • Genome annotation: Which tools do we have for it?
    • Rouzé,P., Pavy,N. and Rombauts,S. (1999) Genome annotation: which tools do we have for it? Curr. Opin. Plant Biol., 2, 90-95.
    • (1999) Curr. Opin. Plant Biol , vol.2 , pp. 90-95
    • Rouzé, P.1    Pavy, N.2    Rombauts, S.3
  • 10
    • 0030218799 scopus 로고    scopus 로고
    • Finding genes by computer: The state of the art
    • Fickett,J.W. (1996) Finding genes by computer: the state of the art. Trends Genet., 12, 316-320.
    • (1996) Trends Genet , vol.12 , pp. 316-320
    • Fickett, J.W.1
  • 11
    • 0030768930 scopus 로고    scopus 로고
    • Computational methods for the identification of genes in vertebrate genomic sequences
    • Claverie,J.M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet., 6, 1735-1744.
    • (1997) Hum. Mol. Genet , vol.6 , pp. 1735-1744
    • Claverie, J.M.1
  • 12
    • 0031298797 scopus 로고    scopus 로고
    • Computational gene identification: An open problem
    • Guigó,R. (1997) Computational gene identification: an open problem. Comput. Chem., 21, 215-222.
    • (1997) Comput. Chem , vol.21 , pp. 215-222
    • Guigó, R.1
  • 13
    • 11544300316 scopus 로고    scopus 로고
    • Computational genefinding
    • Haussler,D. (1998) Computational genefinding. Trends Biochem. Sci., 12-15.
    • (1998) Trends Biochem. Sci , pp. 12-15
    • Haussler, D.1
  • 14
    • 0032104509 scopus 로고    scopus 로고
    • Finding the genes in genomic DNA
    • Burge,C. and Karlin,S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol., 8, 346-354.
    • (1998) Curr. Opin. Struct. Biol , vol.8 , pp. 346-354
    • Burge, C.1    Karlin, S.2
  • 15
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset,M. and Guigó,R. (1996) Evaluation of gene structure prediction programs. Genomics, 34, 353-367.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigó, R.2
  • 16
    • 0035002807 scopus 로고    scopus 로고
    • Evaluation of gene-finding programs on mammalian sequences
    • Rogic,S., Mackworth,A. and Ouellette,F. (2001) Evaluation of gene-finding programs on mammalian sequences. Genome Res., 11, 817-832.
    • (2001) Genome Res , vol.11 , pp. 817-832
    • Rogic, S.1    Mackworth, A.2    Ouellette, F.3
  • 17
    • 0033381623 scopus 로고    scopus 로고
    • Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
    • Pavy,N., Rombauts,S., Déhais,P., Mathé,C., Ramana,D.V.V., Leroy,P. and Rouzé,P. (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics, 15, 887-899.
    • (1999) Bioinformatics , vol.15 , pp. 887-899
    • Pavy, N.1    Rombauts, S.2    Déhais, P.3    Mathé, C.4    Ramana, D.V.V.5    Leroy, P.6    Rouzé, P.7
  • 18
    • 0036207282 scopus 로고    scopus 로고
    • Untranslated regions of mRNAs
    • reviews0004.1-0004.10
    • Mignone,F., Gissi,C., Liuni,S. and Pesole,G. (2002) Untranslated regions of mRNAs. Genome Biol., 3, reviews0004.1-0004.10.
    • (2002) Genome Biol , vol.3
    • Mignone, F.1    Gissi, C.2    Liuni, S.3    Pesole, G.4
  • 19
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 21
    • 2642630755 scopus 로고    scopus 로고
    • Analysis of EST-driven gene annotation in human genomic sequence
    • Bailey,L.C., Searls,D.B. and Overton,G.C. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res., 8, 362-376.
    • (1998) Genome Res , vol.8 , pp. 362-376
    • Bailey, L.C.1    Searls, D.B.2    Overton, G.C.3
  • 22
    • 0029259041 scopus 로고
    • ORFs and genes: How strong a connection?
    • Fickett,J.W. (1995) ORFs and genes: how strong a connection? J. Comput. Biol., 2, 117-123.
    • (1995) J. Comput. Biol , vol.2 , pp. 117-123
    • Fickett, J.W.1
  • 23
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett J.W. and Tung,C.S. (1992) Assessment of protein coding measures. Nucleic Acids Res., 20, 6441-6450.
    • (1992) Nucleic Acids Res , vol.20 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.S.2
  • 24
    • 0026623434 scopus 로고
    • The prediction of exons through an analysis of spliceable open reading frames
    • Hutchinson,G.B. and Hayden,M.R. (1992) The prediction of exons through an analysis of spliceable open reading frames. Nucleic Acids Res., 20, 3453-3462.
    • (1992) Nucleic Acids Res , vol.20 , pp. 3453-3462
    • Hutchinson, G.B.1    Hayden, M.R.2
  • 25
    • 0001785052 scopus 로고
    • GenView: A computing tool for protein-coding regions prediction in nucleotide sequences
    • Lim,H.A., Fickett,J.W., Cantor,C.R. and Robbins,R.J. (eds), Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. World Scientific Publishing, Singapore
    • Milanesi,L., Kolchanov,N.A., Rogozin,I.B., Ischenko,I.V., Kel,A.E., Orlov,Y.L., Ponomarenko,M.P. and Vezzoni,P. (1993) GenView: a computing tool for protein-coding regions prediction in nucleotide sequences. In Lim,H.A., Fickett,J.W., Cantor,C.R. and Robbins,R.J. (eds), Proceedings of the Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis. World Scientific Publishing, Singapore, pp. 573-588.
    • (1993) , pp. 573-588
    • Milanesi, L.1    Kolchanov, N.A.2    Rogozin, I.B.3    Ischenko, I.V.4    Kel, A.E.5    Orlov, Y.L.6    Ponomarenko, M.P.7    Vezzoni, P.8
  • 26
    • 0031027525 scopus 로고    scopus 로고
    • Identification of protein coding regions in the human genome by quadratic discriminant analysis
    • [Erratum (1997) Proc. Natl Acad. Sci. USA, 94, 5495]
    • Zhang,M.Q. (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl Acad. Sci. USA, 94, 565-568. [Erratum (1997) Proc. Natl Acad. Sci. USA, 94, 5495]
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 565-568
    • Zhang, M.Q.1
  • 27
    • 0028965444 scopus 로고
    • Identification of protein coding regions in genomic DNA
    • Snyder,E.E. and Stormo,G.D. (1995) Identification of protein coding regions in genomic DNA. J. Mol. Biol., 248, 1-18.
    • (1995) J. Mol. Biol , vol.248 , pp. 1-18
    • Snyder, E.E.1    Stormo, G.D.2
  • 28
    • 0030627562 scopus 로고    scopus 로고
    • The Gene-Finder computer tools for analysis of human and model organisms genome sequences
    • Gaasterland,T., Karp,P., Karplus,K. Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA
    • Solovyev,V. and Salamov,A. (1997) The Gene-Finder computer tools for analysis of human and model organisms genome sequences. In Gaasterland,T., Karp,P., Karplus,K. Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 294-302.
    • (1997) , pp. 294-302
    • Solovyev, V.1    Salamov, A.2
  • 29
    • 0000241874 scopus 로고
    • GENMARK: Parallel gene recognition for both DNA strands
    • Borodovsky,M. and McIninch,J. (1993) GENMARK: 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.2
  • 30
    • 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
  • 31
    • 84959057192 scopus 로고    scopus 로고
    • EuGène: An eukaryotic gene finder that combines several sources of evidence
    • Gascuel,O. and Sagot,M.-F. (eds), First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000. Springer-Verlag, Germany
    • Schiex,T., Moisan,A. and Rouzé,P. (2001) EuGène: an eukaryotic gene finder that combines several sources of evidence. In Gascuel,O. and Sagot,M.-F. (eds), Lecture Notes in Computer Science, Vol. 2006, First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000. Springer-Verlag, Germany, pp. 111-125.
    • (2001) Lecture Notes in Computer Science , vol.2006 , pp. 111-125
    • Schiex, T.1    Moisan, A.2    Rouzé, P.3
  • 32
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • Salzberg,S. Delcher,A. 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.1    Delcher, A.2    Kasif, S.3    White, O.4
  • 35
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene findings
    • Lukashin,A.V. and Borodovsky,M. (1998) GeneMark.hmm: new solutions for gene findings. Nucleic Acids Res., 26, 1107-1115.
    • (1998) Nucleic Acids Res , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 36
    • 0024805395 scopus 로고
    • The isochore organization of the human genome
    • Bernardi,G. (1989) The isochore organization of the human genome. Annu. Rev. Genet., 23, 637-661.
    • (1989) Annu. Rev. Genet , vol.23 , pp. 637-661
    • Bernardi, G.1
  • 37
    • 0025361547 scopus 로고
    • Gene distribution and isochore organization in the nuclear genome of plants
    • Montero,L.M., Salinas,J., Malassi,G. and Bernardi,G. (1990) Gene distribution and isochore organization in the nuclear genome of plants. Nucleic Acids Res., 18, 1859-1867.
    • (1990) Nucleic Acids Res , vol.18 , pp. 1859-1867
    • Montero, L.M.1    Salinas, J.2    Malassi, G.3    Bernardi, G.4
  • 38
    • 0028963020 scopus 로고
    • Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores
    • Duret,L., Mouchiroud,D. and Gautier,C. (1995) Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol., 40, 308-317.
    • (1995) J. Mol. Evol , vol.40 , pp. 308-317
    • Duret, L.1    Mouchiroud, D.2    Gautier, C.3
  • 39
    • 0030787856 scopus 로고    scopus 로고
    • Analysis of donor splice signals in different organisms
    • Rogozin,I.B., and Milanesi,L. (1997) Analysis of donor splice signals in different organisms. J. Mol. Evol., 45, 50-59.
    • (1997) J. Mol. Evol , vol.45 , pp. 50-59
    • Rogozin, I.B.1    Milanesi, L.2
  • 40
    • 0029822410 scopus 로고    scopus 로고
    • Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences
    • Kleffe,J., Hermann,K., Vahrson,W., Wittig,B. and Brendel,V. (1996) Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucleic Acids Res., 24, 4709-4718.
    • (1996) Nucleic Acids Res , vol.24 , pp. 4709-4718
    • Kleffe, J.1    Hermann, K.2    Vahrson, W.3    Wittig, B.4    Brendel, V.5
  • 41
    • 0025744474 scopus 로고
    • Prediction of human mRNA donor and acceptor sites from the DNA sequence
    • Brunak,S., Engelbrecht,J. and Knudsen,S. (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol., 220, 49-65.
    • (1991) J. Mol. Biol , vol.220 , pp. 49-65
    • Brunak, S.1    Engelbrecht, J.2    Knudsen, S.3
  • 42
    • 0029791403 scopus 로고    scopus 로고
    • Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information
    • Hebsgaard,S.M., Korning,P.G., Tolstrup,N., Engelbrecht,J., Rouzé,P. and Brunak,S. (1996) Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information. Nucleic Acids Res., 24, 3439-3452.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3439-3452
    • Hebsgaard, S.M.1    Korning, P.G.2    Tolstrup, N.3    Engelbrecht, J.4    Rouzé, P.5    Brunak, S.6
  • 43
    • 0030878280 scopus 로고    scopus 로고
    • A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
    • Tolstrup,N., Rouzé,P. and Brunak,S. (1997) A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites. Nucleic Acids Res., 25, 3159-3163.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3159-3163
    • Tolstrup, N.1    Rouzé, P.2    Brunak, S.3
  • 45
    • 0027377256 scopus 로고
    • A weight array method for splicing signal analysis
    • Zhang,M.Q. and Marr,T.G. (1993) A weight array method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
    • (1993) Comput. Appl. Biosci , vol.9 , pp. 499-509
    • Zhang, M.Q.1    Marr, T.G.2
  • 46
    • 0030869663 scopus 로고    scopus 로고
    • A method for identifying splice sites and translational start sites in eukaryotic mRNA
    • Salzberg,S.L. (1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci., 13, 365-376.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 365-376
    • Salzberg, S.L.1
  • 47
    • 0030810993 scopus 로고    scopus 로고
    • Finding genes in human DNA with a hidden Markov model
    • Henderson,J., Salzberg,S. and Fasman,K. (1997) Finding genes in human DNA with a hidden Markov model. J. Comput. Biol., 4, 127-141.
    • (1997) J. Comput. Biol , vol.4 , pp. 127-141
    • Henderson, J.1    Salzberg, S.2    Fasman, K.3
  • 49
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications for speech recognition
    • Rabiner,L.R. (1989) A tutorial on hidden Markov models and selected applications for speech recognition. Proc. IEEE, 77, 257-285.
    • (1989) Proc. IEEE , vol.77 , pp. 257-285
    • Rabiner, L.R.1
  • 50
    • 0002430987 scopus 로고    scopus 로고
    • An introduction to hidden Markov models for biological sequences
    • Salzberg,S.L., Searls,D.B. and Kasif,S. (eds), Elsevier, Amsterdam, The Netherlands
    • Krogh,A. (1998) An introduction to hidden Markov models for biological sequences. In Salzberg,S.L., Searls,D.B. and Kasif,S. (eds), Computational Methods in Molecular Biology. Elsevier, Amsterdam, The Netherlands, pp. 46-63.
    • (1998) Computational Methods in Molecular Biology , pp. 46-63
    • Krogh, A.1
  • 51
    • 0036371458 scopus 로고    scopus 로고
    • Pre-mRNA secondary structure prediction aids splice site prediction
    • Altman,R.B., Dunker,A.K., Hunter,L., Lauderdale,K. and Klein,T.E. (eds), World Scientific, Singapore
    • Patterson,D.J., Yasuhara,K. and Ruzzo,W.L. (2002) Pre-mRNA secondary structure prediction aids splice site prediction. In Altman,R.B., Dunker,A.K., Hunter,L., Lauderdale,K. and Klein,T.E. (eds), Pacific Symposium on Biocomputing, Vol. 7, World Scientific, Singapore, pp. 223-234.
    • (2002) Pacific Symposium on Biocomputing , vol.7 , pp. 223-234
    • Patterson, D.J.1    Yasuhara, K.2    Ruzzo, W.L.3
  • 52
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • Ohler,U. and Niemann,H. (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet., 17, 56-60.
    • (2001) Trends Genet , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 53
    • 0033563512 scopus 로고    scopus 로고
    • The biology of eukaryotic promoter prediction - A review
    • Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1999) The biology of eukaryotic promoter prediction - a review. Comput. Chem., 23, 191-207.
    • (1999) Comput. Chem , vol.23 , pp. 191-207
    • Pedersen, A.G.1    Baldi, P.2    Chauvin, Y.3    Brunak, S.4
  • 54
    • 0030627982 scopus 로고    scopus 로고
    • Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis
    • Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), AAAI Press, Menlo Park, CA
    • Pedersen,A.G. and Nielsen,H. (1997) Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis. In Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 226-233.
    • (1997) The Fifth International Conference on Intelligent Systems for Molecular Biology , pp. 226-233
    • Pedersen, A.G.1    Nielsen, H.2
  • 55
    • 0033670134 scopus 로고    scopus 로고
    • Engineering support vector machine kernels that recognize translation initiation sites
    • Zien,A., Ratsch,G., Mika,S., Scholkopf,B., Lengauer,T. and Muller,K. (2000) Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics, 16, 799-807.
    • (2000) Bioinformatics , vol.16 , pp. 799-807
    • Zien, A.1    Ratsch, G.2    Mika, S.3    Scholkopf, B.4    Lengauer, T.5    Muller, K.6
  • 56
    • 0034521884 scopus 로고    scopus 로고
    • Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences
    • Nishikawa,T., Ota,T. and Isogai,T. (2000) Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences. Bioinformatics, 16, 960-967.
    • (2000) Bioinformatics , vol.16 , pp. 960-967
    • Nishikawa, T.1    Ota, T.2    Isogai, T.3
  • 57
    • 0025040574 scopus 로고
    • gm: A practical tool for automating DNA sequence analysis
    • Fields,C.A. and Soderlund,C.A. (1990) gm: a practical tool for automating DNA sequence analysis. Comput. Appl. Biosci., 6, 263-270.
    • (1990) Comput. Appl. Biosci , vol.6 , pp. 263-270
    • Fields, C.A.1    Soderlund, C.A.2
  • 58
    • 0025000924 scopus 로고
    • Computer prediction of the exon-intron structure of mammalian pre-mRNAs
    • Gelfand,M.S. (1990) Computer prediction of the exon-intron structure of mammalian pre-mRNAs. Nucleic Acids Res., 18, 5865-5869.
    • (1990) Nucleic Acids Res , vol.18 , pp. 5865-5869
    • Gelfand, M.S.1
  • 60
    • 0030628597 scopus 로고    scopus 로고
    • Dynamite; a flexible code generating language for dynamic programming methods need in sequence comparison
    • Birney,E. and Durbin,R. (1997) Dynamite; a flexible code generating language for dynamic programming methods need in sequence comparison. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 56-64.
    • (1997) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.5 , pp. 56-64
    • Birney, E.1    Durbin, R.2
  • 61
    • 0029955046 scopus 로고    scopus 로고
    • Gene structure prediction using information on homologous protein sequence
    • Rogozin,I.B. Milanesi,L. and Kolchanov,N.A. (1996) Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci., 12, 161-170.
    • (1996) Comput. Appl. Biosci , vol.12 , pp. 161-170
    • Rogozin, I.B.1    Milanesi, L.2    Kolchanov, N.A.3
  • 62
    • 0034129662 scopus 로고    scopus 로고
    • Homology-based gene structure prediction: Simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
    • Gotoh,O. (2000) Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics, 16, 190-202.
    • (2000) Bioinformatics , vol.16 , pp. 190-202
    • Gotoh, O.1
  • 63
    • 0031878236 scopus 로고    scopus 로고
    • Finding intron/exon splice junctions using INFO. INterruption Finder and Organizer
    • Laub,M.T. and Smith,D.W. (1998) Finding intron/exon splice junctions using INFO. INterruption Finder and Organizer. J. Comput. Biol., 5, 307-321.
    • (1998) J. Comput. Biol , vol.5 , pp. 307-321
    • Laub, M.T.1    Smith, D.W.2
  • 65
    • 0034047754 scopus 로고    scopus 로고
    • Detection of protein coding sequences using a mixture model for local protein amino acid sequence
    • Thayer,E., Bystroff,C. and Baker,D. (2000) Detection of protein coding sequences using a mixture model for local protein amino acid sequence. J. Comput. Biol., 7, 317-327.
    • (2000) J. Comput. Biol , vol.7 , pp. 317-327
    • Thayer, E.1    Bystroff, C.2    Baker, D.3
  • 66
    • 0031573382 scopus 로고    scopus 로고
    • A tool for analyzing and annotating genomic sequences
    • Huang,X., Adams,M.D., Zhou,H. and Kerlavage,A.R. (1997) A tool for analyzing and annotating genomic sequences. Genomics, 46, 37-45.
    • (1997) Genomics , vol.46 , pp. 37-45
    • Huang, X.1    Adams, M.D.2    Zhou, H.3    Kerlavage, A.R.4
  • 67
    • 0034646570 scopus 로고    scopus 로고
    • Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring
    • Usuka,J. and Brendel,V. (2000) Gene structure prediction by spliced alignment of genomic DNA with protein sequences: increased accuracy by differential splice site scoring. J. Mol. Biol., 297, 1075-1085.
    • (2000) J. Mol. Biol , vol.297 , pp. 1075-1085
    • Usuka, J.1    Brendel, V.2
  • 68
    • 0034129194 scopus 로고    scopus 로고
    • Optimal spliced alignment of homologous cDNA to a genomic DNA template
    • Usuka,J., Zhu,W. and Brendel,V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics, 16, 203-211.
    • (2000) Bioinformatics , vol.16 , pp. 203-211
    • Usuka, J.1    Zhu, W.2    Brendel, V.3
  • 69
    • 0031732094 scopus 로고    scopus 로고
    • A computer program for aligning a cDNA sequence with a genomic DNA sequence
    • Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8, 967-974.
    • (1998) Genome Res , vol.8 , pp. 967-974
    • Florea, L.1    Hartzell, G.2    Zhang, Z.3    Rubin, G.M.4    Miller, W.5
  • 70
    • 0035189310 scopus 로고    scopus 로고
    • Spidey: A tool for mRNA-to-genomic alignments
    • Wheelan,S.J., Church,D.M. and Ostell,J.M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res., 11, 1952-1957.
    • (2001) Genome Res , vol.11 , pp. 1952-1957
    • Wheelan, S.J.1    Church, D.M.2    Ostell, J.M.3
  • 71
    • 0033373273 scopus 로고    scopus 로고
    • Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database
    • Fukunishi,Y., Suzuki,H., Yoshino,M., Konno,H. and Hayashizaki,Y. (1999) Prediction of human cDNA from its homologous mouse full-length cDNA and human shotgun database. FEBS Lett., 464, 129-132.
    • (1999) FEBS Lett , vol.464 , pp. 129-132
    • Fukunishi, Y.1    Suzuki, H.2    Yoshino, M.3    Konno, H.4    Hayashizaki, Y.5
  • 72
    • 0033534799 scopus 로고    scopus 로고
    • Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences
    • Rogozin,I.B., D'Angelo,D. and Milanesi,L. (1999) Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences. Gene, 226, 129-137.
    • (1999) Gene , vol.226 , pp. 129-137
    • Rogozin, I.B.1    D'Angelo, D.2    Milanesi, L.3
  • 73
    • 0031954877 scopus 로고    scopus 로고
    • EbEST: An automated tool using expressed sequence tags to delineate gene structure
    • Jiang,J. and Jacob,H.J. (1998) EbEST: an automated tool using expressed sequence tags to delineate gene structure. Genome Res., 8, 268-275.
    • (1998) Genome Res , vol.8 , pp. 268-275
    • Jiang, J.1    Jacob, H.J.2
  • 74
    • 0030870076 scopus 로고    scopus 로고
    • ESTNOME: A program to align spliced DNA sequences to unspliced genomic DNA
    • Mott,R. (1997) ESTNOME: a program to align spliced DNA sequences to unspliced genomic DNA. Comput. Appl. Biosci., 13, 477-478.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 477-478
    • Mott, R.1
  • 75
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • Kan,Z., Rouchka,E.C., Gish,W.R. and States,D.J. (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res., 11, 889-900.
    • (2001) Genome Res , vol.11 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 77
    • 0033832676 scopus 로고    scopus 로고
    • Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
    • Kent,W.J. and Zahler,A.M. (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res., 10, 1115-1125.
    • (2000) Genome Res , vol.10 , pp. 1115-1125
    • Kent, W.J.1    Zahler, A.M.2
  • 79
    • 0033636013 scopus 로고    scopus 로고
    • A space-efficient algorithm for aligning large genomic sequences
    • Morgenstern,B. (2000) A space-efficient algorithm for aligning large genomic sequences. Bioinformatics, 16, 948-949.
    • (2000) Bioinformatics , vol.16 , pp. 948-949
    • Morgenstern, B.1
  • 80
    • 0033861549 scopus 로고    scopus 로고
    • Human and mouse gene structure: Comparative analysis and application to exon prediction
    • Batzoglou,S., Pachter,L., Mesirov,J., Berger,B. and Lander,E.S. (2000) Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res., 10, 950-958.
    • (2000) Genome Res , vol.10 , pp. 950-958
    • Batzoglou, S.1    Pachter, L.2    Mesirov, J.3    Berger, B.4    Lander, E.S.5
  • 81
    • 0034565167 scopus 로고    scopus 로고
    • The conserved exon method for gene finding
    • Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Scheeff,E., Smith,C., Strande,S. and Weissig,H. (eds), AAAI Press, Menlo Park, CA
    • Bafna,V. and Huson,D. (2000) The conserved exon method for gene finding. In Bourne,P., Gribskov,M., Altman,R., Jensen,N., Hope,D., Lengauer,T., Mitchell,J., Scheeff,E., Smith,C., Strande,S. and Weissig,H. (eds), Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 3-12.
    • (2000) Eighth International Conference on Intelligent Systems for Molecular Biology , pp. 3-12
    • Bafna, V.1    Huson, D.2
  • 82
    • 0034832202 scopus 로고    scopus 로고
    • SGP-1: Prediction and validation of homologous genes based on sequence alignments
    • Wiehe,T., Gebauer-Jung,S., Mitchell-Olds,T. and Guigo,R. (2001) SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res., 11, 1574-1583.
    • (2001) Genome Res , vol.11 , pp. 1574-1583
    • Wiehe, T.1    Gebauer-Jung, S.2    Mitchell-Olds, T.3    Guigo, R.4
  • 83
    • 0035177648 scopus 로고    scopus 로고
    • Gene recognition in eukaryotic DNA by comparison of genomic sequences
    • Novichkov,P.S., Gelfand,M.S. and Mironov,A.A. (2001) Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinformatics, 17, 1011-1018.
    • (2001) Bioinformatics , vol.17 , pp. 1011-1018
    • Novichkov, P.S.1    Gelfand, M.S.2    Mironov, A.A.3
  • 84
    • 85009205020 scopus 로고    scopus 로고
    • Orphan gene finding - An exon assembly approach
    • in press
    • Blayo,P., Rouzé,P. and Sagot,M.-F. (2002) Orphan gene finding - an exon assembly approach. Theor. Comput. Sci., in press.
    • (2002) Theor. Comput. Sci
    • Blayo, P.1    Rouzé, P.2    Sagot, M.-F.3
  • 85
    • 0036112213 scopus 로고    scopus 로고
    • Applications of generalized pair hidden Markov models to alignment and gene finding problems
    • Pachter,L., Alexandersson,M. and Cawley,S. (2002) Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol., 9, 389-399.
    • (2002) J. Comput. Biol , vol.9 , pp. 389-399
    • Pachter, L.1    Alexandersson, M.2    Cawley, S.3
  • 86
    • 0030094146 scopus 로고    scopus 로고
    • CENSOR - A program for identification and elimination of repetitive elements from DNA sequences
    • Jurka,J., Klonowski,P., Dagman,V. and Pelton,P. (1996) CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem., 20, 119-112.
    • (1996) Comput. Chem , vol.20 , pp. 112-119
    • Jurka, J.1    Klonowski, P.2    Dagman, V.3    Pelton, P.4
  • 87
  • 88
    • 0032456609 scopus 로고    scopus 로고
    • Assembling genes from predicted exons in linear time with dynamic programming
    • Guigó,R. (1998) Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol., 5, 681-702.
    • (1998) J. Comput. Biol , vol.5 , pp. 681-702
    • Guigó, R.1
  • 90
    • 0028605559 scopus 로고
    • Constructing gene models from accurately predicted exons: An application of dynamic programming
    • Xu,Y., Mural,R.J. and Uberbaker,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    Mural, R.J.2    Uberbaker, E.C.3
  • 91
    • 17344390287 scopus 로고    scopus 로고
    • Gene recognition based on DAG shortest paths
    • Chuang,J.S. and Roth,D. (2001) Gene recognition based on DAG shortest paths. Bioinformatics, 1, 1-9.
    • (2001) Bioinformatics , vol.1 , pp. 1-9
    • Chuang, J.S.1    Roth, D.2
  • 92
    • 0031825707 scopus 로고    scopus 로고
    • GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences
    • Kleffe,J., Hermann,K., Vahrson,W., Wittig,B. and Brendel,V. (1998) GeneGenerator-a flexible algorithm for gene prediction and its application to maize sequences. Bioinformatics, 14, 232-243.
    • (1998) Bioinformatics , vol.14 , pp. 232-243
    • Kleffe, J.1    Hermann, K.2    Vahrson, W.3    Wittig, B.4    Brendel, V.5
  • 93
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimal decoding algorithm
    • Viterbi,A. (1967) Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Informat. Theor., IT-13, 260-269.
    • (1967) IEEE Trans. Informat. Theor , vol.13 IT , pp. 260-269
    • Viterbi, A.1
  • 94
    • 0003787146 scopus 로고
    • Princeton University Press, Princeton, NJ
    • Bellman,R.E. (1957) Dynamic Programming. Princeton University Press, Princeton, NJ.
    • (1957) Dynamic Programming
    • Bellman, R.E.1
  • 95
    • 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
  • 96
    • 0030333286 scopus 로고    scopus 로고
    • A generalized Hidden Markov Model for the recognition of human genes in DNA
    • States,D.J., Agarwal,P., Gaasterland,T., Hunter,L. and Smith,R.F. (eds), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA
    • Kulp,D., Haussler,D., Reese,M.G. and 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. and Smith,R.F. (eds), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 134-142.
    • (1996) , pp. 134-142
    • Kulp, D.1    Haussler, D.2    Reese, M.G.3    Eeckman, F.H.4
  • 97
    • 0033931903 scopus 로고    scopus 로고
    • Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment
    • Hooper,P., Zhang,H. and Wishart,D. (2000) Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment. Bioinformatics, 16, 425-438.
    • (2000) Bioinformatics , vol.16 , pp. 425-438
    • Hooper, P.1    Zhang, H.2    Wishart, D.3
  • 98
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performace of a HMM and their application for gene finding
    • Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), AAAI Press, Menlo Park, CA
    • Krogh,A. (1997) Two methods for improving performace of a HMM and their application for gene finding. In Gaasterland,T., Karp,P., Karplus,K., Ouzounis,C., Sander,C. and Valencia,A. (eds), The Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 179-186.
    • (1997) The Fifth International Conference on Intelligent Systems for Molecular Biology , pp. 179-186
    • Krogh, A.1
  • 99
    • 0035002015 scopus 로고    scopus 로고
    • Computational inference of homologous gene structures in the human genome
    • Yeh,R.-F., Lim,L.P. and Burge,C.B. (2001) Computational inference of homologous gene structures in the human genome. Genome Res., 11, 803-816.
    • (2001) Genome Res , vol.11 , pp. 803-816
    • Yeh, R.-F.1    Lim, L.P.2    Burge, C.B.3
  • 100
    • 17444437765 scopus 로고    scopus 로고
    • Integrating genomic homology into gene structure prediction
    • Korf,I., Flicek,P., Duan,D. and Brent,M.R. (2001) Integrating genomic homology into gene structure prediction. Bioinformatics, 17, S140-S148.
    • (2001) Bioinformatics , vol.17
    • Korf, I.1    Flicek, P.2    Duan, D.3    Brent, M.R.4
  • 101
    • 0031761144 scopus 로고    scopus 로고
    • Gene recognition by combination of several gene-finding programs
    • Murakami,K. and Tagaki,T. (1998) Gene recognition by combination of several gene-finding programs. Bioinformatics, 14, 665-675.
    • (1998) Bioinformatics , vol.14 , pp. 665-675
    • Murakami, K.1    Tagaki, T.2
  • 102
    • 0032944241 scopus 로고    scopus 로고
    • INFOGENE: A database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects
    • Solovyev,V.V. and Salamov,A.A. (1999) INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects. Nucleic Acids Res., 27, 248-250.
    • (1999) Nucleic Acids Res , vol.27 , pp. 248-250
    • Solovyev, V.V.1    Salamov, A.A.2
  • 103
    • 0036173326 scopus 로고    scopus 로고
    • A Bayesian framework for combining gene predictions
    • Pavlovic,V., Garg,A. and Kasif,S. (2002) A Bayesian framework for combining gene predictions. Bioinformatics, 18, 19-27.
    • (2002) Bioinformatics , vol.18 , pp. 19-27
    • Pavlovic, V.1    Garg, A.2    Kasif, S.3
  • 104
    • 0030881249 scopus 로고    scopus 로고
    • Genotator: A workbench for sequence annotation
    • Harris,N.L. (1997) Genotator: a workbench for sequence annotation. Genome Res., 7, 754-762.
    • (1997) Genome Res , vol.7 , pp. 754-762
    • Harris, N.L.1
  • 105
    • 0029828166 scopus 로고    scopus 로고
    • Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture
    • Gaasterland,T. and Sensen,C.W. (1996) Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie, 78, 302-310.
    • (1996) Biochimie , vol.78 , pp. 302-310
    • Gaasterland, T.1    Sensen, C.W.2
  • 107
    • 0034742461 scopus 로고    scopus 로고
    • Identifying the 3′-terminal exon in human DNA
    • Tabaska,J. Davuluri,R. and Zhang,M. (2001) Identifying the 3′-terminal exon in human DNA. Bioinformatics, 17, 602-607.
    • (2001) Bioinformatics , vol.17 , pp. 602-607
    • Tabaska, J.1    Davuluri, R.2    Zhang, M.3
  • 108
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • Davuluri,R.V. Groose,I. and Zhang,M.Q. (2001) Computational identification of promoters and first exons in the human genome. Nature Genet., 29, 412-417.
    • (2001) Nature Genet , vol.29 , pp. 412-417
    • Davuluri, R.V.1    Groose, I.2    Zhang, M.Q.3
  • 109
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res., 12, 458-461.
    • (2002) Genome Res , vol.12 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.2
  • 110
    • 0033598805 scopus 로고    scopus 로고
    • In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species
    • Graber,J.H., Canter,C.R., Molar,S.C. and Smith,T.F. (1999) In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc. Natl Acad. USA, 96, 14055-14060.
    • (1999) Proc. Natl Acad. USA , vol.96 , pp. 14055-14060
    • Graber, J.H.1    Canter, C.R.2    Molar, S.C.3    Smith, T.F.4
  • 111
    • 0033782834 scopus 로고    scopus 로고
    • An assessment of gene prediction accuracy in large DNA sequences
    • Guigó,R. Agarwal,P., Abril,J., Burset,M. and Fickett,J. (2000) An assessment of gene prediction accuracy in large DNA sequences. Genome Res, 10, 1631-1642.
    • (2000) Genome Res , vol.10 , pp. 1631-1642
    • Guigó, R.1    Agarwal, P.2    Abril, J.3    Burset, M.4    Fickett, J.5
  • 113
    • 0027280998 scopus 로고
    • Strong conservation of vertebrate non-coding sequences during vertebrate evolution: Potential involvement in post-transcriptional regulation of gene expression
    • Duret,L., Dorkeld,F. and Gautier,C. (1993) Strong conservation of vertebrate non-coding sequences during vertebrate evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res., 21, 2315-2322.
    • (1993) Nucleic Acids Res , vol.21 , pp. 2315-2322
    • Duret, L.1    Dorkeld, F.2    Gautier, C.3
  • 114
    • 0032884653 scopus 로고    scopus 로고
    • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
    • Jareborg,N., Birney,E. and Durbin,R. (1999) Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res., 9, 815-824.
    • (1999) Genome Res , vol.9 , pp. 815-824
    • Jareborg, N.1    Birney, E.2    Durbin, R.3
  • 115
    • 0032722057 scopus 로고    scopus 로고
    • OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana
    • Quesada,V., Ponce,M.R. and Micol,J.L. (1999) OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana. FEBS Lett., 461, 101-106.
    • (1999) FEBS Lett , vol.461 , pp. 101-106
    • Quesada, V.1    Ponce, M.R.2    Micol, J.L.3
  • 116
    • 0022475084 scopus 로고
    • Gene within a gene: Nested Drosophila genes encode unrelated proteins on opposite DNA strands
    • Henikoff,S., Keene,M.A., Fechtel,K. and Fristrom,J.W. (1986) Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands. Cell, 44, 33-42.
    • (1986) Cell , vol.44 , pp. 33-42
    • Henikoff, S.1    Keene, M.A.2    Fechtel, K.3    Fristrom, J.W.4
  • 117
    • 0030749116 scopus 로고    scopus 로고
    • Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic presnoRNAs
    • Leader,D.J., Clark,G.P., Watters,J., Beven,A.F., Shaw,P.J. and Brown,J.W. (1997) Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic presnoRNAs. EMBO J., 16, 5742-5751.
    • (1997) EMBO J , vol.16 , pp. 5742-5751
    • Leader, D.J.1    Clark, G.P.2    Watters, J.3    Beven, A.F.4    Shaw, P.J.5    Brown, J.W.6
  • 118
    • 0032103829 scopus 로고    scopus 로고
    • Gene clusters and polycistronic transcription in eukaryotes
    • Blumenthal,T. (1998) Gene clusters and polycistronic transcription in eukaryotes. Bioessays, 20, 480-487.
    • (1998) Bioessays , vol.20 , pp. 480-487
    • Blumenthal, T.1
  • 119
    • 0035113035 scopus 로고    scopus 로고
    • Pro-Frame: Similarity-based gene recognition in eukaryotic DNA sequences with errors
    • Mironov,A.A., Novichkov,P.S. and Gelfand,M.S. (2001) Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics, 17, 13-15.
    • (2001) Bioinformatics , vol.17 , pp. 13-15
    • Mironov, A.A.1    Novichkov, P.S.2    Gelfand, M.S.3
  • 120
    • 0029134925 scopus 로고
    • A frameshift error detection algorithm for DNA sequencing projects
    • Fichant,G.A. and Quentin,Y. (1995) A frameshift error detection algorithm for DNA sequencing projects. Nucleic Acids Res., 23, 2900-2908.
    • (1995) Nucleic Acids Res , vol.23 , pp. 2900-2908
    • Fichant, G.A.1    Quentin, Y.2
  • 122
    • 0033290515 scopus 로고    scopus 로고
    • ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
    • Iseli,C., Jongeneel,C.V. and Bucher,P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 138-148.
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol , pp. 138-148
    • Iseli, C.1    Jongeneel, C.V.2    Bucher, P.3
  • 123
    • 0032570603 scopus 로고    scopus 로고
    • Cloning and characterization of promoter and 5′-UTR of the NMDA receptor subunit epsilon 2: Evidence for alternative splicing of 5′-noncoding exon
    • Klein,M., Pieri,I., Uhlmann,F., Pfizenmaier,K. and Eisel,U. (1998) Cloning and characterization of promoter and 5′-UTR of the NMDA receptor subunit epsilon 2: evidence for alternative splicing of 5′-noncoding exon, Gene, 208, 259-269.
    • (1998) Gene , vol.208 , pp. 259-269
    • Klein, M.1    Pieri, I.2    Uhlmann, F.3    Pfizenmaier, K.4    Eisel, U.5
  • 124
    • 0031456850 scopus 로고    scopus 로고
    • Classification of introns: U2-type or U12-type
    • Sharp,P.A. and Burge,C.B. (1997) Classification of introns: U2-type or U12-type. Cell, 91, 875-879.
    • (1997) Cell , vol.91 , pp. 875-879
    • Sharp, P.A.1    Burge, C.B.2
  • 125
    • 0034326362 scopus 로고    scopus 로고
    • Analysis of canonical and non-canonical splice sites in mammalian genomes
    • Burset,M., Seledtsov,I. and Solovyev,V. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res., 28, 4364-4375.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4364-4375
    • Burset, M.1    Seledtsov, I.2    Solovyev, V.3
  • 126
    • 0034029236 scopus 로고    scopus 로고
    • ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
    • Croft,L., Schandorff,S., Clark.F., Burrage,K., Arctander,P. and Mattick,J. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet., 24, 340-341.
    • (2000) Nature Genet , vol.24 , pp. 340-341
    • Croft, L.1    Schandorff, S.2    Clark, F.3    Burrage, K.4    Arctander, P.5    Mattick, J.6
  • 127
    • 0035393343 scopus 로고    scopus 로고
    • Genome-wide detection of alternative splicing in expressed sequences of human genes
    • Modrek,B., Resch,A., Grasso,C. and Lee,C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29, 2850-2859.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2850-2859
    • Modrek, B.1    Resch, A.2    Grasso, C.3    Lee, C.4
  • 128
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nature Genet., 30, 13-19.
    • (2002) Nature Genet , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 129
    • 0035370845 scopus 로고    scopus 로고
    • Pre-mRNA splicing in the new millennium
    • Hastings,M.L. and Krainer,A.R. (2001) Pre-mRNA splicing in the new millennium. Curr. Opin. Cell Biol., 13, 302-309.
    • (2001) Curr. Opin. Cell Biol , vol.13 , pp. 302-309
    • Hastings, M.L.1    Krainer, A.R.2
  • 130
    • 0031859991 scopus 로고    scopus 로고
    • Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering
    • Gautheret,D., Poirot,O., Lopez,F., Audic,S. and Claverie Jean,M. (1998) Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res., 8, 524-530.
    • (1998) Genome Res , vol.8 , pp. 524-530
    • Gautheret, D.1    Poirot, O.2    Lopez, F.3    Audic, S.4    Claverie Jean, M.5
  • 131
    • 0033061571 scopus 로고    scopus 로고
    • Initiation of translation in prokaryotes and eukaryotes
    • Kozak,M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
    • (1999) Gene , vol.234 , pp. 187-208
    • Kozak, M.1
  • 132
    • 0033513099 scopus 로고    scopus 로고
    • Non-AUG initiation of AGAMOUS mRNA translation in Arabidpsis thaliana
    • Riechmann,J.L., Ito,T. and Meyerowitz,E. (1999) Non-AUG initiation of AGAMOUS mRNA translation in Arabidpsis thaliana. Mol. Cell. Biol., 19, 8505-8512.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 8505-8512
    • Riechmann, J.L.1    Ito, T.2    Meyerowitz, E.3
  • 133
    • 0030474826 scopus 로고    scopus 로고
    • Translation of CUG but not AUG-initiated forms of human fibroblast growth factor 2 is activated in transformed and stressed cells
    • Vagner,S., Touriol,C., Galy,B., Audigier,S., Gensac,M. Amalric,F., Bayard,F., Prats,H. and Prats,A. (1996) Translation of CUG but not AUG-initiated forms of human fibroblast growth factor 2 is activated in transformed and stressed cells. J. Cell Biol., 135, 1391-1402.
    • (1996) J. Cell Biol , vol.135 , pp. 1391-1402
    • Vagner, S.1    Touriol, C.2    Galy, B.3    Audigier, S.4    Gensac, M.5    Amalric, F.6    Bayard, F.7    Prats, H.8    Prats, A.9
  • 134
    • 0032544103 scopus 로고    scopus 로고
    • Self-identification of protein-coding regions in microbial genomes
    • Audic,S. and Claverie,J.-M. (1998) Self-identification of protein-coding regions in microbial genomes. Proc. Natl Acad. Sci. USA, 95, 10026-10031.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 10026-10031
    • Audic, S.1    Claverie, J.-M.2
  • 135
    • 0033214628 scopus 로고    scopus 로고
    • Heuristic approach to deriving models for gene finding
    • Besemer,J. and Borodovsky,M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res., 27, 3911-3920.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3911-3920
    • Besemer, J.1    Borodovsky, M.2
  • 136
    • 0026332291 scopus 로고
    • Evidence for horizontal gene transfer in Escherichia coli speciation
    • Médigue,C., Rouxel,T., Vigier,P., Hénaut,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
    • Médigue, C.1    Rouxel, T.2    Vigier, P.3    Hénaut, A.4    Danchin, A.5
  • 137
    • 0033524964 scopus 로고    scopus 로고
    • Classification of Arabidopsis thaliana gene sequences: Clustering of coding sequences into two groups according to codon usage improves gene prediction
    • Mathé,C., Peresetsky,A., Déhais,P., Van Montagu,M. and Rouzé,P. (1999) Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction. J. Mol. Biol., 285, 1977-1991.
    • (1999) J. Mol. Biol , vol.285 , pp. 1977-1991
    • Mathé, C.1    Peresetsky, A.2    Déhais, P.3    Van Montagu, M.4    Rouzé, P.5
  • 139
    • 0032415865 scopus 로고    scopus 로고
    • How to interpret an anonymous bacterial genome: Machine learning approach to gene identification
    • Hayes,W.S. and Borodovsky,M. (1998) How to interpret an anonymous bacterial genome: machine learning approach to gene identification. Genome Res., 8, 1154-1171.
    • (1998) Genome Res , vol.8 , pp. 1154-1171
    • Hayes, W.S.1    Borodovsky, M.2
  • 140
    • 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
    • Besemer,J., Lomsadze,A. and Borodovsky,M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2607-2618
    • Besemer, J.1    Lomsadze A. Borodovsky, M.2
  • 142
    • 0033569629 scopus 로고    scopus 로고
    • Keeping genome databases clean and up to date
    • Pennisi,E. (1999) Keeping genome databases clean and up to date. Science, 286, 447-450.
    • (1999) Science , vol.286 , pp. 447-450
    • Pennisi, E.1
  • 143
    • 0032127026 scopus 로고    scopus 로고
    • Functional genomics-bioinformatics is ready for the challenge
    • Smith,T.F. (1998) Functional genomics-bioinformatics is ready for the challenge. Trends Genet., 14, 291-293.
    • (1998) Trends Genet , vol.14 , pp. 291-293
    • Smith, T.F.1
  • 144
    • 0034887203 scopus 로고    scopus 로고
    • The Gene Ontology Consortium Creating the gene ontology resource: Design and implementation
    • The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res., 11, 1425-1433.
    • (2001) Genome Res , vol.11 , pp. 1425-1433
  • 145
    • 0035098865 scopus 로고    scopus 로고
    • On the importance of standardisation in life sciences
    • Brazma,A. (2001) On the importance of standardisation in life sciences. Bioinformatics, 17, 113-114.
    • (2001) Bioinformatics , vol.17 , pp. 113-114
    • Brazma, A.1
  • 146
    • 0035011227 scopus 로고    scopus 로고
    • Comparison of genomic DNA sequences: Solved and unsolved problems
    • Miller,W. (2001) Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics, 17, 391-397.
    • (2001) Bioinformatics , vol.17 , pp. 391-397
    • Miller, W.1
  • 147
    • 0034707216 scopus 로고    scopus 로고
    • Genomic scrap yard: How genomes utilize all that junk
    • Makalowski,W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene, 259, 61-67.
    • (2000) Gene , vol.259 , pp. 61-67
    • Makalowski, W.1
  • 148
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of concerved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
    • Bergman,C. and Kreitman,M. (2001) Analysis of concerved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome, Res., 11, 1335-1345.
    • (2001) Genome, Res , vol.11 , pp. 1335-1345
    • Bergman, C.1    Kreitman, M.2
  • 149
    • 0032785505 scopus 로고    scopus 로고
    • Noncoding RNA genes
    • Eddy,S.R. (1999) Noncoding RNA genes. Curr. Opin. Genet. Dev., 9, 695-699.
    • (1999) Curr. Opin. Genet. Dev , vol.9 , pp. 695-699
    • Eddy, S.R.1
  • 151
    • 0033765362 scopus 로고    scopus 로고
    • Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
    • Rivas,E. and Eddy,S. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16, 583-605.
    • (2000) Bioinformatics , vol.16 , pp. 583-605
    • Rivas, E.1    Eddy, S.2
  • 152
    • 0035282695 scopus 로고    scopus 로고
    • GeneSplicer: A new computational method for splice site prediction
    • Pertea,M., Lin,X. and Salzberg,S. (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res., 29, 1185-1190.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1185-1190
    • Pertea, M.1    Lin, X.2    Salzberg, S.3
  • 153
    • 0032512716 scopus 로고    scopus 로고
    • Prediction of splice sites in plant pre-mRNA from sequence properties
    • Brendel,V., Kleffe.J., Carle Urioste,J.C. and Walbot, V. (1998) Prediction of splice sites in plant pre-mRNA from sequence properties. J. Mol. Biol., 276, 85-104.
    • (1998) J. Mol. Biol , vol.276 , pp. 85-104
    • Brendel, V.1    Kleffe, J.2    Carle Urioste, J.C.3    Walbot, V.4
  • 154
    • 0027944162 scopus 로고
    • Gene structure prediction by linguistic methods
    • Dong,S and Searls,D.B. (1994) Gene structure prediction by linguistic methods, Genomics, 23, 540-551.
    • (1994) Genomics , vol.23 , pp. 540-551
    • Dong, S.1    Searls, D.B.2
  • 155
    • 0030786488 scopus 로고    scopus 로고
    • Automated gene identification in large-scale genomic sequences
    • Xu,Y.X. and Uberbacher,E.C. (1997) Automated gene identification in large-scale genomic sequences. J. Comput. Biol., 4, 325-338.
    • (1997) J. Comput. Biol , vol.4 , pp. 325-338
    • Xu, Y.X.1    Uberbacher, E.C.2
  • 156
    • 77957187566 scopus 로고
    • A probabilistic model for detecting coding regions in DNA sequences
    • Thomas,A. and Skolnick,M.H. (1994) A probabilistic model for detecting coding regions in DNA sequences. IMA J. Math. Appl. Med. Biol., 11, 149-160.
    • (1994) IMA J. Math. Appl. Med. Biol , vol.11 , pp. 149-160
    • Thomas, A.1    Skolnick, M.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.