메뉴 건너뛰기




Volumn 2, Issue 3, 2008, Pages 310-321

Signal processing in sequence analysis: Advances in eukaryotic gene prediction

Author keywords

Autoregressive processes; Correlation; Deoxyribonucleic acid (DNA); Discrete cosine transforms (DCTs); Discrete Fourier transforms (DFTs); Gaussian mixture models

Indexed keywords

DATA PROCESSING; DIGITAL SIGNAL PROCESSING; DNA; FORECASTING; GENES; INDUSTRIAL RESEARCH; NUCLEIC ACIDS; ORGANIC ACIDS; SENSITIVITY ANALYSIS; SIGNAL PROCESSING; STANDARDS;

EID: 47049101156     PISSN: 19324553     EISSN: None     Source Type: Journal    
DOI: 10.1109/JSTSP.2008.923854     Document Type: Article
Times cited : (143)

References (62)
  • 3
    • 0034061137 scopus 로고    scopus 로고
    • GeneID in drosophila
    • G. Parra, E. Blanco, and R. Guigo, "GeneID in drosophila," Genome Res., vol. 10, no. 4, pp. 511-515, 2000.
    • (2000) Genome Res , vol.10 , Issue.4 , pp. 511-515
    • Parra, G.1    Blanco, E.2    Guigo, R.3
  • 4
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • A. V. Lukashin and M. Borodovsky, "GeneMark.hmm: New solutions for gene finding," Nucl. Acids Res., vol. 26, no. 4, pp. 1107-1115, 1998.
    • (1998) Nucl. Acids Res , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 6
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structure in human genomic DNA
    • C. Burge and S. Karlin, "Prediction of complete gene structure in human genomic DNA," J. Mol. Biol., vol. 268, no. 1, pp. 78-94, 1997.
    • (1997) J. Mol. Biol , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 7
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performance of an HMM and their applications for gene-finding
    • A. Krogh, "Two methods for improving performance of an HMM and their applications for gene-finding," in Proc. 5th Int. Conf. Intelligent Systems for Molecular Biology, 1997, pp. 179-186.
    • (1997) Proc. 5th Int. Conf. Intelligent Systems for Molecular Biology , pp. 179-186
    • Krogh, A.1
  • 8
    • 0032449018 scopus 로고    scopus 로고
    • A decision tree system for finding genes in DNA
    • S. Salzberg, A. L. Delcher, K. H. Fasman, and J. Henderson, "A decision tree system for finding genes in DNA," J. Comput. Biol., vol. 5, no. 4, pp. 667-680, 1998.
    • (1998) J. Comput. Biol , vol.5 , Issue.4 , pp. 667-680
    • Salzberg, S.1    Delcher, A.L.2    Fasman, K.H.3    Henderson, J.4
  • 9
    • 0031027525 scopus 로고    scopus 로고
    • Identification of protein coding regions in the human genome by quadratic discriminant analysis
    • M. Q. Zhang, "Identification of protein coding regions in the human genome by quadratic discriminant analysis," Proc. Nat. Acad. Sci. vol. 94, no. 2, pp. 565-568, 1997.
    • (1997) Proc. Nat. Acad. Sci , vol.94 , Issue.2 , pp. 565-568
    • Zhang, M.Q.1
  • 10
    • 0030585734 scopus 로고    scopus 로고
    • Evaluation of gene structure prediction programs
    • M. Burset and R. Guigo, "Evaluation of gene structure prediction programs," Genomics, vol. 34, pp. 353-367, 1996.
    • (1996) Genomics , vol.34 , pp. 353-367
    • Burset, M.1    Guigo, R.2
  • 11
    • 0035002807 scopus 로고    scopus 로고
    • Evaluation of gene-finding programs on mammalian sequences
    • S. Rogic, A. K. Mackworth, and B. F. Ouellette, "Evaluation of gene-finding programs on mammalian sequences," Genome Res., vol. 11, no. 5, pp. 817-832, 2001.
    • (2001) Genome Res , vol.11 , Issue.5 , pp. 817-832
    • Rogic, S.1    Mackworth, A.K.2    Ouellette, B.F.3
  • 12
    • 0036596123 scopus 로고    scopus 로고
    • Computer programs for eukaryotic gene prediction
    • V. Makarov, "Computer programs for eukaryotic gene prediction," Briefings Bioinf., vol. 3, no. 2, pp. 195-199, 2002.
    • (2002) Briefings Bioinf , vol.3 , Issue.2 , pp. 195-199
    • Makarov, V.1
  • 13
    • 26944466382 scopus 로고    scopus 로고
    • Evaluation and fuzzy classification of gene finding programs on human genome sequences
    • A. Nagar, S. Purushothaman, and H. Tawfik, "Evaluation and fuzzy classification of gene finding programs on human genome sequences," FSKD, pp. 821-829, 2005.
    • (2005) FSKD , pp. 821-829
    • Nagar, A.1    Purushothaman, S.2    Tawfik, H.3
  • 15
    • 33847329566 scopus 로고    scopus 로고
    • In search of the short ones: Improved prediction of short exons in vertebrates, plants, fungi and protists
    • Y. Saeys, P. Rouze, and Y. V. de Peer, "In search of the short ones: Improved prediction of short exons in vertebrates, plants, fungi and protists," Bioinformatics, vol. 23, no. 4, pp. 414-420, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 414-420
    • Saeys, Y.1    Rouze, P.2    de Peer, Y.V.3
  • 16
    • 0031761144 scopus 로고    scopus 로고
    • Gene recognition by combination of several gene-finding programs
    • K. Murakami and T. Takagi, "Gene recognition by combination of several gene-finding programs," Bioinformatics, vol. 14, no. 8, pp. 665-675, 1998.
    • (1998) Bioinformatics , vol.14 , Issue.8 , pp. 665-675
    • Murakami, K.1    Takagi, T.2
  • 17
    • 0036173326 scopus 로고    scopus 로고
    • A Bayesian framework for combining gene predictions
    • V. Pavlovic, A. Garg, and S. Kasif, "A Bayesian framework for combining gene predictions," Bioinformatics, vol. 18, no. 1, pp. 19-27, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 19-27
    • Pavlovic, V.1    Garg, A.2    Kasif, S.3
  • 18
    • 85032750863 scopus 로고    scopus 로고
    • Genomic signal processing
    • Apr
    • D. Anastassiou, "Genomic signal processing," IEEE Signal Process. Mag., vol. 18, no. 4, pp. 8-20, Apr. 2001.
    • (2001) IEEE Signal Process. Mag , vol.18 , Issue.4 , pp. 8-20
    • Anastassiou, D.1
  • 20
    • 0000204878 scopus 로고
    • Evolution of long-range fractal correlations and 1/f noise in DNA base sequences
    • R. F. Voss, "Evolution of long-range fractal correlations and 1/f noise in DNA base sequences," Phy. Rev. Lett., vol. 68, no. 25, pp. 3805-3808, 1992.
    • (1992) Phy. Rev. Lett , vol.68 , Issue.25 , pp. 3805-3808
    • Voss, R.F.1
  • 21
    • 0027995001 scopus 로고
    • Z curves, an intuitive tool for visualizing and analyzing the DNA sequences
    • R. Zhang and C. T. Zhang, "Z curves, an intuitive tool for visualizing and analyzing the DNA sequences," J. Biomol. Struct. Dyn., vol. 11, no. 4, pp. 767-782, 1994.
    • (1994) J. Biomol. Struct. Dyn , vol.11 , Issue.4 , pp. 767-782
    • Zhang, R.1    Zhang, C.T.2
  • 22
    • 0023043752 scopus 로고
    • A measure of DNA periodicity
    • B. D. Silverman and R. Linsker, "A measure of DNA periodicity," J. Theor. Biol., vol. 118, pp. 295-300, 1986.
    • (1986) J. Theor. Biol , vol.118 , pp. 295-300
    • Silverman, B.D.1    Linsker, R.2
  • 24
    • 33646821759 scopus 로고    scopus 로고
    • Symbol-balanced quaternionic periodicity transform for latent pattern detection in DNA sequences
    • A. K. Brodzik and O. Peters, "Symbol-balanced quaternionic periodicity transform for latent pattern detection in DNA sequences," in Proc. IEEE ICASSP, 2005, vol. 5, pp. v/373-v/376.
    • (2005) Proc. IEEE ICASSP , vol.5
    • Brodzik, A.K.1    Peters, O.2
  • 26
    • 47049097236 scopus 로고    scopus 로고
    • Signal processing for biologically-inspired gradient source localization and DNA sequence analysis,
    • Ph.D. dissertation, Georgia Inst. Technol, Atlanta
    • G. L. Rosen, "Signal processing for biologically-inspired gradient source localization and DNA sequence analysis," Ph.D. dissertation, Georgia Inst. Technol., Atlanta, 2006.
    • (2006)
    • Rosen, G.L.1
  • 27
    • 75949086882 scopus 로고    scopus 로고
    • Visualization of genomic data using inter-nucleotide distance signals
    • presented at the
    • A. S. S. Nair and T. Mahalakshmi, "Visualization of genomic data using inter-nucleotide distance signals," presented at the IEEE Int. Conf. Genomic Signal Processing, 2005.
    • (2005) IEEE Int. Conf. Genomic Signal Processing
    • Nair, A.S.S.1    Mahalakshmi, T.2
  • 28
    • 0002065556 scopus 로고    scopus 로고
    • Equivalence of two Fourier methods for biological sequences
    • E. Coward, "Equivalence of two Fourier methods for biological sequences," J. Math. Biol., vol. 36, pp. 64-70, 1997.
    • (1997) J. Math. Biol , vol.36 , pp. 64-70
    • Coward, E.1
  • 29
    • 0036503714 scopus 로고    scopus 로고
    • Computing linear transforms of symbolic signals
    • Mar
    • W. Wang and D. H. Johnson, "Computing linear transforms of symbolic signals," IEEE Trans. Signal Process., vol. 50, no. 3, pp. 628-634, Mar. 2002.
    • (2002) IEEE Trans. Signal Process , vol.50 , Issue.3 , pp. 628-634
    • Wang, W.1    Johnson, D.H.2
  • 30
    • 0032001783 scopus 로고    scopus 로고
    • 3-, 10.5-, 200- and 400-base periodicities in genome sequences
    • E. N. Trifonov, "3-, 10.5-, 200- and 400-base periodicities in genome sequences," Phys. A, vol. 249, pp. 511-516, 1998.
    • (1998) Phys. A , vol.249 , pp. 511-516
    • Trifonov, E.N.1
  • 31
    • 0020480512 scopus 로고
    • Recognition of protein coding regions in DNA sequences
    • J. W. Fickett, "Recognition of protein coding regions in DNA sequences," Nucl. Acids Res., vol. 10, pp. 5303-5318, 1982.
    • (1982) Nucl. Acids Res , vol.10 , pp. 5303-5318
    • Fickett, J.W.1
  • 33
    • 0042525755 scopus 로고    scopus 로고
    • Gene prediction by spectral rotation measure: A new method for identifying protein-coding regions
    • D. Kotlar and Y. Lavner, "Gene prediction by spectral rotation measure: A new method for identifying protein-coding regions," Genome Res. vol. 18, pp. 1930-1937, 2003.
    • (2003) Genome Res , vol.18 , pp. 1930-1937
    • Kotlar, D.1    Lavner, Y.2
  • 34
    • 11244304236 scopus 로고    scopus 로고
    • Detection of 3-periodicity for small genomic sequences based on AR techniques
    • N. Rao and S. J. Shepherd, "Detection of 3-periodicity for small genomic sequences based on AR techniques," in Proc. IEEE Int. Conf. Comm., Circuits Syst., 2004, vol. 2, pp. 1032-1036.
    • (2004) Proc. IEEE Int. Conf. Comm., Circuits Syst , vol.2 , pp. 1032-1036
    • Rao, N.1    Shepherd, S.J.2
  • 37
    • 0002268541 scopus 로고
    • An algorithm for the evaluation of finite trigonometric series
    • G. Goertzel, "An algorithm for the evaluation of finite trigonometric series," Amer. Math. Monthly, vol. 65, no. 1, pp. 34-35, 1958.
    • (1958) Amer. Math. Monthly , vol.65 , Issue.1 , pp. 34-35
    • Goertzel, G.1
  • 38
    • 43949156767 scopus 로고
    • Understanding long-range correlations in DNA sequences
    • W. Li and T. G. Marr, "Understanding long-range correlations in DNA sequences," Phys. D, vol. 75, pp. 392-416, 1994.
    • (1994) Phys. D , vol.75 , pp. 392-416
    • Li, W.1    Marr, T.G.2
  • 39
    • 5244285298 scopus 로고    scopus 로고
    • Correlations in DNA sequences: The role of protein coding segments
    • H. Herzel and I. Große, "Correlations in DNA sequences: The role of protein coding segments," Phys. Rev. E, vol. 55, no. 1, pp. 800-810, 1997.
    • (1997) Phys. Rev. E , vol.55 , Issue.1 , pp. 800-810
    • Herzel, H.1    Große, I.2
  • 40
    • 0031298464 scopus 로고    scopus 로고
    • The study of correlation structure of DNA sequences: A critical review
    • W. Li, "The study of correlation structure of DNA sequences: A critical review," Comput. Chem., vol. 21, no. 4, pp. 257-271, 1997.
    • (1997) Comput. Chem , vol.21 , Issue.4 , pp. 257-271
    • Li, W.1
  • 43
    • 0036550319 scopus 로고    scopus 로고
    • Conversion of nucleotides sequences into genomic signals
    • P. D. Cristea, "Conversion of nucleotides sequences into genomic signals," J. Cell. Mol. Med., vol. 6, no. 2, pp. 279-303, 2002.
    • (2002) J. Cell. Mol. Med , vol.6 , Issue.2 , pp. 279-303
    • Cristea, P.D.1
  • 44
    • 33646786796 scopus 로고    scopus 로고
    • A fast DFT based gene prediction algorithm for identification of protein coding regions
    • S. Datta and A. Asif, "A fast DFT based gene prediction algorithm for identification of protein coding regions," in Proc. IEEE ICASSP, 2005, vol. 5, pp. 653-656.
    • (2005) Proc. IEEE ICASSP , vol.5 , pp. 653-656
    • Datta, S.1    Asif, A.2
  • 45
    • 0003415703 scopus 로고    scopus 로고
    • Identification of genes in human genomic DNA,
    • Ph.D. dissertation, Stanford Univ, Stanford, CA
    • C. Burge, "Identification of genes in human genomic DNA," Ph.D. dissertation, Stanford Univ., Stanford, CA, 1997.
    • (1997)
    • Burge, C.1
  • 46
    • 34547493930 scopus 로고    scopus 로고
    • Time and frequency domain methods for gene and exon prediction in eukaryotes
    • M. Akhtar and J. E. E. Ambikairajah, "Time and frequency domain methods for gene and exon prediction in eukaryotes," in Proc. IEEE ICASSP 2007, pp. 573-576.
    • (2007) Proc. IEEE ICASSP , pp. 573-576
    • Akhtar, M.1    Ambikairajah, J.E.E.2
  • 50
    • 0020849649 scopus 로고
    • The time-domain periodogram algorithm
    • E. Ambikairajah and M. J. Carey, "The time-domain periodogram algorithm," Signal Process., vol. 5, pp. 491-513, 1983.
    • (1983) Signal Process , vol.5 , pp. 491-513
    • Ambikairajah, E.1    Carey, M.J.2
  • 51
    • 0000068037 scopus 로고    scopus 로고
    • Robust method for periodicity detection and characterization of irregular cyclical series in terms of embedded periodic components
    • P. P. Kanjilal, J. Bhattacharya, and G. Saha, "Robust method for periodicity detection and characterization of irregular cyclical series in terms of embedded periodic components," Phys. Rev. E, vol. 59, no. 4, pp. 4013-4025, 1999.
    • (1999) Phys. Rev. E , vol.59 , Issue.4 , pp. 4013-4025
    • Kanjilal, P.P.1    Bhattacharya, J.2    Saha, G.3
  • 52
    • 33845318542 scopus 로고    scopus 로고
    • Detection of period-3 behavior in genomic sequences using singular value decomposition
    • M. Akhtar, E. Ambikairajah, and J. Epps, "Detection of period-3 behavior in genomic sequences using singular value decomposition," in Proc. IEEE Int. Conf. Emerging Technologies, 2005, pp. 13-17.
    • (2005) Proc. IEEE Int. Conf. Emerging Technologies , pp. 13-17
    • Akhtar, M.1    Ambikairajah, E.2    Epps, J.3
  • 56
    • 0021760026 scopus 로고
    • Computer methods to locate signals in nucleic acid sequences
    • R. Staden, "Computer methods to locate signals in nucleic acid sequences," Nucl. Acids Res., vol. 12, pp. 505-519, 1984.
    • (1984) Nucl. Acids Res , vol.12 , pp. 505-519
    • Staden, R.1
  • 57
    • 61649085735 scopus 로고    scopus 로고
    • Modeling dependencies in pre-mRNA splicing signals
    • S. L. Salzberg, D. B. Searls, and S. Kasif, Eds. New York: Elsevier, ch. 8, pp
    • C. Burge, "Modeling dependencies in pre-mRNA splicing signals," in Computational Methods in Molecular Biology, S. L. Salzberg, D. B. Searls, and S. Kasif, Eds. New York: Elsevier, 1998, ch. 8, pp. 129-164.
    • (1998) Computational Methods in Molecular Biology , pp. 129-164
    • Burge, C.1
  • 58
    • 0027377256 scopus 로고
    • A weight array method for splicing signal analysis
    • M. Q. Zhang and T. G. Marr, "A weight array method for splicing signal analysis," CABIOS, vol. 9, no. 5, pp. 499-509, 1993.
    • (1993) CABIOS , vol.9 , Issue.5 , pp. 499-509
    • Zhang, M.Q.1    Marr, T.G.2
  • 59
    • 0030869663 scopus 로고    scopus 로고
    • A method for identifying splice sites and translational start sites in eukaryotic mRNA
    • S. L. Salzberg, "A method for identifying splice sites and translational start sites in eukaryotic mRNA," Comput. Appl. Biosci. vol. 13, no. 4, pp. 365-376, 1997.
    • (1997) Comput. Appl. Biosci , vol.13 , Issue.4 , pp. 365-376
    • Salzberg, S.L.1
  • 61
    • 33947667789 scopus 로고    scopus 로고
    • Gene identification using the Z-curve representation
    • A. Rushdi and J. Tuqan, "Gene identification using the Z-curve representation," in Proc. IEEE ICASSP, 2006, vol. 2, pp. 1024-1027.
    • (2006) Proc. IEEE ICASSP , vol.2 , pp. 1024-1027
    • Rushdi, A.1    Tuqan, J.2
  • 62
    • 49049089800 scopus 로고    scopus 로고
    • Optimizing period-3 methods for eukaryotic gene prediction
    • M. Akhtar, E. Ambikairajah, and J. Epps, "Optimizing period-3 methods for eukaryotic gene prediction," in Proc. IEEE ICASSP, 2008, pp. 621-624.
    • (2008) Proc. IEEE ICASSP , pp. 621-624
    • Akhtar, M.1    Ambikairajah, E.2    Epps, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.