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Volumn 34, Issue 3, 1996, Pages 353-367

Evaluation of gene structure prediction programs

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE STRUCTURE; PREDICTION; PRIORITY JOURNAL; VERTEBRATE;

EID: 0030585734     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1996.0298     Document Type: Article
Times cited : (583)

References (47)
  • 3
    • 0000241874 scopus 로고
    • GENMARK: Parallel gene recognition for both DNA strands
    • Borodovsky, M. Y., and McIninch, J. D. (1993). GENMARK: Parallel gene recognition for both DNA strands. Comput. Chem. 17: 123-133.
    • (1993) Comput. Chem. , vol.17 , pp. 123-133
    • Borodovsky, M.Y.1    McIninch, J.D.2
  • 4
    • 0028004414 scopus 로고
    • Intrinsic and extrinsic approaches for detecting genes in a bacterial genome
    • Borodovsky, M. Y., Rudd, K. E., and Koonin, E. V. (1994). Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucleic Acids Res. 22: 4756-4767.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4756-4767
    • Borodovsky, M.Y.1    Rudd, K.E.2    Koonin, E.V.3
  • 5
    • 0029062198 scopus 로고
    • Identification and analysis of multigene families by comparison of exon fingerprints
    • Brown, N. P., Whittaker, A. J., and Newell, W. R. (1995). Identification and analysis of multigene families by comparison of exon fingerprints. J. Mol. Biol. 249: 342-359.
    • (1995) J. Mol. Biol. , vol.249 , pp. 342-359
    • Brown, N.P.1    Whittaker, A.J.2    Newell, W.R.3
  • 6
    • 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
  • 7
    • 0025317956 scopus 로고
    • k-tuple frequency analysis: From intron/exon discrimination to T-cell epitope mapping
    • Claverie, J.-M., Sauvaget, I., and Bougueleret, L. (1990). k-tuple frequency analysis: From intron/exon discrimination to T-cell epitope mapping. Methods Enzymol. 183: 237-252.
    • (1990) Methods Enzymol. , vol.183 , pp. 237-252
    • Claverie, J.-M.1    Sauvaget, I.2    Bougueleret, L.3
  • 8
    • 0001923233 scopus 로고
    • Survey of new data and computer methods of analysis
    • National Biomedical Research Foundation, Washington, DC
    • Dayhoff, M. O. (1978). Survey of new data and computer methods of analysis. In "Atlas of Protein Sequence and Structure," Suppl. 5, Vol. 3, pp. 1-8, National Biomedical Research Foundation, Washington, DC.
    • (1978) Atlas of Protein Sequence and Structure , vol.3 , Issue.SUPPL. 5 , pp. 1-8
    • Dayhoff, M.O.1
  • 9
    • 0028307348 scopus 로고
    • 8 Genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmatic intermediate filament proteins in the nematode Caenorhabditis elegans
    • Dodemont, H., Riemer, D., Ledger, N., and Weber, K. (1994). 8 genes and alternative RNA processing pathways generate an unexpectedly large diversity of cytoplasmatic intermediate filament proteins in the nematode Caenorhabditis elegans. EMBO J. 13: 2625-2638.
    • (1994) EMBO J. , vol.13 , pp. 2625-2638
    • Dodemont, H.1    Riemer, D.2    Ledger, N.3    Weber, K.4
  • 10
    • 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
  • 11
    • 0025864008 scopus 로고
    • Identifying potential tRNA genes in genomic DNA sequences
    • Fichant, G. A., and Burks, C. (1991). Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220: 659-671.
    • (1991) J. Mol. Biol. , vol.220 , pp. 659-671
    • Fichant, G.A.1    Burks, C.2
  • 12
    • 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
  • 13
    • 0020480512 scopus 로고
    • Recognition of protein coding regions in DNA sequences
    • Fickett, J. W. (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.W.1
  • 14
    • 0000377189 scopus 로고    scopus 로고
    • The gene identification problem: An overview for developers
    • Fickett, J. W. (1996). The gene identification problem: An overview for developers. Comput. Chem. 20: 103-118.
    • (1996) Comput. Chem. , vol.20 , pp. 103-118
    • Fickett, J.W.1
  • 15
    • 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
  • 16
    • 0011787003 scopus 로고    scopus 로고
    • Computational gene identification
    • S. Swindell, R. Miller, and G. Myers, Eds., Horizon Scientific Press, Oxford
    • Fickett, J. W., and Guigó, R. (1996). Computational gene identification. In "Internet for the Molecular Biologist" (S. Swindell, R. Miller, and G. Myers, Eds.), Horizon Scientific Press, Oxford.
    • (1996) Internet for the Molecular Biologist
    • Fickett, J.W.1    Guigó, R.2
  • 17
    • 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
  • 18
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of haemophilus influenzae Rd.
    • Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus Influenzae Rd. Science 269: 496-512.
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3    Clayton, R.A.4
  • 19
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
    • (1995) Science , vol.270 , pp. 397-403
    • Fraser, C.M.1    Gocayne, J.D.2    White, O.3    Adams, M.D.4
  • 20
    • 0025000924 scopus 로고
    • Computer prediction of exon-intron structure of mammalian pre-mRNAs
    • Gelfand, M. S. (1990). Computer prediction of 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
  • 21
    • 0029258948 scopus 로고
    • Prediction of function in DNA sequence analysis
    • Gelfand, M. S. (1995). Prediction of function in DNA sequence analysis. J. Comput. Biol. 1: 87-115.
    • (1995) J. Comput. Biol. , vol.1 , pp. 87-115
    • Gelfand, M.S.1
  • 22
    • 0027234853 scopus 로고
    • Prediction of the exon-intron structure by a dynamic programming approach
    • Gelfand, M. S., and Roytberg, M. A. (1993). Prediction of the exon-intron structure by a dynamic programming approach. Biosystems 30: 173-182.
    • (1993) Biosystems , vol.30 , pp. 173-182
    • Gelfand, M.S.1    Roytberg, M.A.2
  • 23
    • 0027399530 scopus 로고
    • Identification of protein coding regions by database similarity search
    • Gish, W., and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nature Genet. 3: 266-272.
    • (1993) Nature Genet. , vol.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 25
    • 0028850576 scopus 로고
    • Distinctive sequence features in protein coding, genic noncoding, and intergenic human DNA
    • Guigó, R., and Fickett, J. W. (1995). Distinctive sequence features in protein coding, genic noncoding, and intergenic human DNA. J. Mol. Biol. 253: 51-60.
    • (1995) J. Mol. Biol. , vol.253 , pp. 51-60
    • Guigó, R.1    Fickett, J.W.2
  • 26
    • 0027249597 scopus 로고
    • Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene
    • Guo, W., Worley, K., Adams, V., Mason, J., et al. (1993). Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene. Nature Genet. 4: 367-372.
    • (1993) Nature Genet. , vol.4 , pp. 367-372
    • Guo, W.1    Worley, K.2    Adams, V.3    Mason, J.4
  • 27
    • 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
  • 29
    • 0028020523 scopus 로고
    • Evaluation of the exons predictions of the GRAIL software
    • Lopez, R. S., Larsen, F., and Prydz, H. (1994). Evaluation of the exons predictions of the GRAIL software. Genomics 24: 133-136.
    • (1994) Genomics , vol.24 , pp. 133-136
    • Lopez, R.S.1    Larsen, F.2    Prydz, H.3
  • 30
    • 0029005101 scopus 로고
    • Emphasis turns from mapping to large-scale sequencing
    • Marshall, E. (1995). Emphasis turns from mapping to large-scale sequencing. Science 268: 1270-1271.
    • (1995) Science , vol.268 , pp. 1270-1271
    • Marshall, E.1
  • 33
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers, E. W., and Miller, W. (1988). Optimal alignments in linear space. Comput. Appl. Biosci. 4: 11-17.
    • (1988) Comput. Appl. Biosci. , vol.4 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 34
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson, W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183: 63-98.
    • (1990) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 35
    • 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
  • 36
    • 0000635560 scopus 로고
    • Computer based exon detection: An evaluation metric for comparison
    • Singh, G. B., and Krawetz, S. A. (1994). Computer based exon detection: An evaluation metric for comparison. Int. J. Genome Res. 1: 321-338.
    • (1994) Int. J. Genome Res. , vol.1 , pp. 321-338
    • Singh, G.B.1    Krawetz, S.A.2
  • 38
    • 0027229632 scopus 로고
    • Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural networks
    • Snyder, E. E., and Stormo, G. D. (1993). Identification of coding regions in genomic DNA sequences: An application of dynamic programming and neural networks. Nucleic Acids Res. 21: 607-613.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 607-613
    • Snyder, E.E.1    Stormo, G.D.2
  • 39
    • 0028965444 scopus 로고
    • Identification of protein coding regions in genomic DNA
    • Snyder, E. E., and Stormo, G. D. (1995a). 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
  • 41
    • 0028618270 scopus 로고
    • Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames
    • Solovyev, V. V., Salamov, A. A., and Lawrence, C. B. (1994). Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Res. 22: 5156-5163.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5156-5163
    • Solovyev, V.V.1    Salamov, A.A.2    Lawrence, C.B.3
  • 42
    • 0028401927 scopus 로고
    • Combined use of sequence similarity and codon bias for coding region identification
    • States, D. J., and Gish, W. (1994). Combined use of sequence similarity and codon bias for coding region identification. J. Comput. Biol. 1: 39-50.
    • (1994) J. Comput. Biol. , vol.1 , pp. 39-50
    • States, D.J.1    Gish, W.2
  • 43
    • 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
  • 44
    • 0026351408 scopus 로고
    • Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach
    • Uberbacher, E. C., and Mural, R. J. (1991). Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA 88: 11261-11265.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 11261-11265
    • Uberbacher, E.C.1    Mural, R.J.2
  • 46
    • 0028605559 scopus 로고
    • Constructing gene models from accurately predicted exons: An application of dynamic programming
    • Xu, Y., Mural, R. J., and Uberbacher, E. C. (1994b). 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    Uberbacher, E.C.3
  • 47
    • 0029075793 scopus 로고
    • Correcting sequencing errors in DNA coding regions using a dynamic programming approach
    • Xu, Y., Mural, R. J., and Uberbacher, E. C. (1995). Correcting sequencing errors in DNA coding regions using a dynamic programming approach. Comput. Appl. Biosci. 11: 117-124.
    • (1995) Comput. Appl. Biosci. , vol.11 , pp. 117-124
    • Xu, Y.1    Mural, R.J.2    Uberbacher, E.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.