메뉴 건너뛰기




Volumn 268, Issue 1, 1997, Pages 78-94

Prediction of complete gene structures in human genomic DNA

Author keywords

Coding sequence; Exon prediction; Gene identification; Probabilistic model; Splice signal

Indexed keywords

DNA;

EID: 0031586003     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0951     Document Type: Article
Times cited : (3310)

References (43)
  • 3
    • 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
  • 4
    • 0027395841 scopus 로고
    • The vertebrate genome: Isochores and evolution
    • Bernard G. The vertebrate genome: isochores and evolution. J. Mol. Evol. 10:1993;186-204.
    • (1993) J. Mol. Evol , vol.10 , pp. 186-204
    • Bernard, G.1
  • 5
    • 0026062392 scopus 로고
    • Does steric interference between splice sites block the splicing of a short c-src neuron-specific exon in non-neuronal cells?
    • Black D. L. Does steric interference between splice sites block the splicing of a short c-src neuron-specific exon in non-neuronal cells? Genes Dev. 5:1991;389-402.
    • (1991) Genes Dev. , vol.5 , pp. 389-402
    • Black, D.L.1
  • 6
    • 0029083530 scopus 로고
    • The turning point in genome research
    • Boguski M. S. The turning point in genome research. Trends Biochem. Sci. 20:1995;295-296.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 295-296
    • Boguski, M.S.1
  • 7
    • 0000241874 scopus 로고
    • GENMARK: Parallel gene recognition for both DNA strands
    • Borodovsky M., McIninch J. GENMARK: parallel gene recognition for both DNA strands. Comp. Chem. 17:1993;123-133.
    • (1993) Comp. Chem. , vol.17 , pp. 123-133
    • Borodovsky, M.1    McIninch, J.2
  • 8
    • 0002425179 scopus 로고
    • PROSET-a fast procedure to create non-redundant sets of protein sequences
    • Brendel V. PROSET-a fast procedure to create non-redundant sets of protein sequences. Math. Comp. Modeling. 16:1992;37-43.
    • (1992) Math. Comp. Modeling , vol.16 , pp. 37-43
    • Brendel, V.1
  • 9
    • 0025278259 scopus 로고
    • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
    • Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212:1990;563-578.
    • (1990) J. Mol. Biol. , vol.212 , pp. 563-578
    • Bucher, P.1
  • 11
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • Burset M., Guigó R. Evaluation of gene structure prediction programs. Genomics. 34:1996;353-367.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigó, R.2
  • 12
    • 0028297002 scopus 로고
    • Large exon size does not limit splicing in vivo
    • Chen I. T., Chasin L. A. Large exon size does not limit splicing in vivo. Mol. Cell. Biol. 14:1994;2140-2146.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 2140-2146
    • Chen, I.T.1    Chasin, L.A.2
  • 13
    • 0026039804 scopus 로고
    • Selection of splice sites in pre-mRNAs with short internal exons
    • Dominski Z., Kole R. Selection of splice sites in pre-mRNAs with short internal exons. Mol. Cell. Biol. 11:1991;6075-6083.
    • (1991) Mol. Cell. Biol. , vol.11 , pp. 6075-6083
    • Dominski, Z.1    Kole, R.2
  • 14
    • 0028963020 scopus 로고
    • Statistical analysis of vertebrate sequences reveals that long genes are scarce in CG-rich isochores
    • Duret L., Mouchiroud D., Gautier C. Statistical analysis of vertebrate sequences reveals that long genes are scarce in CG-rich isochores. J. Mol. Evol. 40:1995;308-317.
    • (1995) J. Mol. Evol. , vol.40 , pp. 308-317
    • Duret, L.1    Mouchiroud, D.2    Gautier, C.3
  • 15
    • 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(8):1996;316-320.
    • (1996) Trends Genet. , vol.128 , pp. 316-320
    • Fickett, J.W.1
  • 16
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett J. W., Tung C.-S. Assessment of protein coding measures. Nucl. Acids Res. 20:1992;6441-6450.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.-S.2
  • 17
    • 0015600423 scopus 로고
    • The Viterbi algorithm
    • Forney G. D. The Viterbi algorithm. Proc. IEEE. 61:1973;268-278.
    • (1973) Proc. IEEE , vol.61 , pp. 268-278
    • Forney, G.D.1
  • 18
    • 0029258948 scopus 로고
    • Prediction of function in DNA sequence analysis
    • Gelfand M. S. Prediction of function in DNA sequence analysis. J. Comp. Biol. 2(1):1995;87-115.
    • (1995) J. Comp. Biol. , vol.21 , pp. 87-115
    • Gelfand, M.S.1
  • 19
    • 0027234853 scopus 로고
    • Prediction of the intron-exon structure by a dynamic programming approach
    • Gelfand M. S., Roytberg M. A. Prediction of the intron-exon structure by a dynamic programming approach. BioSystems. 30:1993;173-182.
    • (1993) BioSystems , vol.30 , pp. 173-182
    • Gelfand, M.S.1    Roytberg, M.A.2
  • 21
    • 0027399530 scopus 로고
    • Identification of protein coding regions by data base similarity search
    • Gish W, States D. J. Identification of protein coding regions by data base similarity search. Nature Genet. 3:1993;266-272.
    • (1993) Nature Genet. , vol.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 23
    • 0025279906 scopus 로고
    • Distribution and consensus of branch point signals in eukaryotic genes: A computerized statistical analysis
    • Harris N. L., Senepathy P. Distribution and consensus of branch point signals in eukaryotic genes: a computerized statistical analysis. Nucl. Acids Res. 18:1990;3015-3019.
    • (1990) Nucl. Acids Res. , vol.18 , pp. 3015-3019
    • Harris, N.L.1    Senepathy, P.2
  • 24
    • 0023685544 scopus 로고
    • A survey on intron and exon lengths
    • Hawkins J. D. A survey on intron and exon lengths. Nucl. Acids Res. 16:1988;9893-9908.
    • (1988) Nucl. Acids Res. , vol.16 , pp. 9893-9908
    • Hawkins, J.D.1
  • 25
    • 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. Comp. Chem. 20(1):1996;119-122.
    • (1996) Comp. Chem. , vol.201 , pp. 119-122
    • Jurka, J.1    Klonowski, P.2    Dagman, V.3    Pelton, P.4
  • 27
    • 0024448304 scopus 로고
    • MyoD is a sequence-specific DNA binding protein requiring a region of myc homology to bind to the muscle creatine kinase enhancer
    • Lasser A. B., Buskin J. N., Lockshon D., Davis R. L., Apone S., Hauschka S. D., Weintraub H. MyoD is a sequence-specific DNA binding protein requiring a region of myc homology to bind to the muscle creatine kinase enhancer. Cell. 58:1989;823-831.
    • (1989) Cell , vol.58 , pp. 823-831
    • Lasser, A.B.1    Buskin, J.N.2    Lockshon, D.3    Davis, R.L.4    Apone, S.5    Hauschka, S.D.6    Weintraub, H.7
  • 28
    • 0028020523 scopus 로고
    • Evaluation of the exon predictions of the GRAIL software
    • Lopez R., Larsen F., Prydz H. Evaluation of the exon predictions of the GRAIL software. Genomics. 24:1994;133-136.
    • (1994) Genomics , vol.24 , pp. 133-136
    • Lopez, R.1    Larsen, F.2    Prydz, H.3
  • 29
    • 0027616365 scopus 로고
    • The role of small nuclear RNAs in RNA splicing
    • McKeown M. The role of small nuclear RNAs in RNA splicing. Curr. Opin. Cell Biol. 5:1993;448-454.
    • (1993) Curr. Opin. Cell Biol. , vol.5 , pp. 448-454
    • McKeown, M.1
  • 30
    • 0029038960 scopus 로고
    • Predicting Pol II promoter sequences using transcription factor binding sites
    • Prestridge D. S. Predicting Pol II promoter sequences using transcription factor binding sites. J. Mol. Biol. 249:1995;923-932.
    • (1995) J. Mol. Biol. , vol.249 , pp. 923-932
    • Prestridge, D.S.1
  • 31
    • 0024610919 scopus 로고
    • A tutorial on Hidden Markov Models and selected applications in speech recognition
    • Rabiner L. R. A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc. IEEE. 77(2):1989;257-285.
    • (1989) Proc. IEEE , vol.772 , pp. 257-285
    • Rabiner, L.R.1
  • 32
    • 0025098474 scopus 로고
    • Exon definition may facilitate splice site selection in RNAs with multiple exons
    • Robberson B. L., Cote G. J., Berget S. M. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10:1990;84-94.
    • (1990) Mol. Cell. Biol. , vol.10 , pp. 84-94
    • Robberson, B.L.1    Cote, G.J.2    Berget, S.M.3
  • 33
    • 0026775484 scopus 로고
    • Efficient optimal decomposition of a sequence into disjoint regions, each matched to some template in an inventory
    • Sankoff D. Efficient optimal decomposition of a sequence into disjoint regions, each matched to some template in an inventory. Math. Biosci. 111:1992;279-293.
    • (1992) Math. Biosci. , vol.111 , pp. 279-293
    • Sankoff, D.1
  • 34
    • 0028965444 scopus 로고
    • Identification of protein coding regions in genomic DNA
    • Snyder E. E., Stormo G. D. Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248:1995;1-18.
    • (1995) J. Mol. Biol. , vol.248 , pp. 1-18
    • Snyder, E.E.1    Stormo, G.D.2
  • 35
    • 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. Nucl. Acid. Res. 22:1994;5156-5163.
    • (1994) Nucl. Acid. Res. , vol.22 , pp. 5156-5163
    • Solovyev, V.V.1    Salamov, A.A.2    Lawrence, C.B.3
  • 36
    • 0021760026 scopus 로고
    • Computer methods to locate signals in nucleic acid sequences
    • Staden R. Computer methods to locate signals in nucleic acid sequences. Nucl. Acids Res. 12:1984;505-519.
    • (1984) Nucl. Acids Res. , vol.12 , pp. 505-519
    • Staden, R.1
  • 39
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimal decoding algorithm
    • Viterbi A. J. Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Trans. Informat. Theory. IT-13:1967;260-269.
    • (1967) IEEE Trans. Informat. Theory , vol.13 , pp. 260-269
    • Viterbi, A.J.1
  • 40
    • 0021704598 scopus 로고
    • A minimal intron length but no specific internal sequence is required for splicing the large rabbit B-globin intron
    • Wieringa B., Hofer E., Weissmann C. A minimal intron length but no specific internal sequence is required for splicing the large rabbit B-globin intron. Cell. 37:1984;915-925.
    • (1984) Cell , vol.37 , pp. 915-925
    • Wieringa, B.1    Hofer, E.2    Weissmann, C.3
  • 41
    • 0029814920 scopus 로고    scopus 로고
    • A segment-based dynamic programming algorithm for predicting gene structure
    • Wu T. A segment-based dynamic programming algorithm for predicting gene structure. J. Comp. Biol. 3(3):1996;375-394.
    • (1996) J. Comp. Biol. , vol.33 , pp. 375-394
    • Wu, T.1
  • 43
    • 0027377256 scopus 로고
    • A weight array method for splicing signal analysis
    • Zhang M. Q., Marr T. G. A weight array method for splicing signal analysis. Comp. Appl. Biol. Sci. 9(5):1993;499-509.
    • (1993) Comp. Appl. Biol. Sci. , vol.95 , pp. 499-509
    • Zhang, M.Q.1    Marr, T.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.