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Volumn 18, Issue 4, 2011, Pages 639-676

Gene prediction based on DNA spectral analysis: A literature review

Author keywords

algorithms; computational molecular biology; DNA computing; DNA spectral analysis; gene finding; machine learning; three base periodicity

Indexed keywords

DNA;

EID: 79957532423     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0184     Document Type: Review
Times cited : (67)

References (55)
  • 1
    • 0035054170 scopus 로고    scopus 로고
    • Statistically optimal null filter based on instantaneous matched processing
    • DOI 10.1007/BF01204921
    • Agarwal, R., Plotkin, E.I., and Swamy, M.N.S. 2001. Statistical optimal null filter based on instantaneous matched processing. Circ. Syst. Signal Process. 20, 37-61. (Pubitemid 32370005)
    • (2001) Circuits, Systems, and Signal Processing , vol.20 , Issue.1 , pp. 37-61
    • Agarwal, R.1    Plotkin, E.I.2    Swamy, M.N.S.3
  • 2
    • 47049101156 scopus 로고    scopus 로고
    • Signal processing in sequence analysis: Advances in eukaryotic gene prediction
    • Akhtar, M., Epps, J., and Ambikairajah, E. 2008a. Signal processing in sequence analysis: advances in eukaryotic gene prediction. IEEE J. Sel. Top. Signal. 2, 310-321.
    • (2008) IEEE J. Sel. Top. Signal. , vol.2 , pp. 310-321
    • Akhtar, M.1    Epps, J.2    Ambikairajah, E.3
  • 3
    • 49049103757 scopus 로고    scopus 로고
    • Digital signal processing techniques for gene finding in eukaryotes
    • Akhtar, M., Ambikairajah, E., and Epps, J. 2008b. Digital signal processing techniques for gene finding in eukaryotes. Lect. Notes Comput. Sci. 5099, 144-152.
    • (2008) Lect. Notes Comput. Sci. , vol.5099 , pp. 144-152
    • Akhtar, M.1    Ambikairajah, E.2    Epps, J.3
  • 7
    • 0034491149 scopus 로고    scopus 로고
    • Frequency-domain analysis of biomolecular sequences
    • Anastassiou, D. 2000. Frequency-domain analysis of biomolecular sequences. Bioinformatics 16, 1073-1081. (Pubitemid 32112000)
    • (2000) Bioinformatics , vol.16 , Issue.12 , pp. 1073-1081
    • Anastassiou, D.1
  • 8
    • 34250648110 scopus 로고    scopus 로고
    • 2D-dynamic representation of DNA sequences
    • DOI 10.1016/j.cplett.2007.05.050, PII S0009261407006379
    • Bielinska-Waz, D., Clark, T., Wa, P., et al. 2007. 2D-dynamic representation of DNA sequences. Chem. Phys. Lett. 442, 140-144. (Pubitemid 46935092)
    • (2007) Chemical Physics Letters , vol.442 , Issue.1-3 , pp. 140-144
    • Bielinska-Waz, D.1    Clark, T.2    Waz, P.3    Nowak, W.4    Nandy, A.5
  • 9
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • DOI 10.1006/jmbi.1997.0951
    • Burge, C., and Karlin, S. 1997. Prediction of complete gene structure in human genomic DNA. J. Mol. Biol. 268, 78-94. (Pubitemid 27192680)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 10
    • 0001913645 scopus 로고
    • Size-dependence of three-periodicity and long-range correlations in DNA sequences
    • Chechetkin, V.R., and Turygin, A.Y. 1995. Size-dependence of three-periodicity and long-range correlations in DNA sequences. Phys. Lett. A 199, 75-80.
    • (1995) Phys. Lett. A , vol.199 , pp. 75-80
    • Chechetkin, V.R.1    Turygin, A.Y.2
  • 12
    • 0036550319 scopus 로고    scopus 로고
    • Conversion of nucleotides sequences into genomic signals
    • Cristea, P.D. 2002. Conversion of nucleotides sequences into genomic signals. J. Cell. Mol. Med. 6, 279-303. (Pubitemid 44133978)
    • (2002) Journal of Cellular and Molecular Medicine , vol.6 , Issue.2 , pp. 279-303
    • Cristea, P.D.1
  • 14
    • 0033178886 scopus 로고    scopus 로고
    • Intron-exon structures of eukaryotic model organisms
    • DOI 10.1093/nar/27.15.3219
    • Deutsch, M., and Long, M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27, 3219-3228. (Pubitemid 29355739)
    • (1999) Nucleic Acids Research , vol.27 , Issue.15 , pp. 3219-3228
    • Deutsch, M.1    Long, M.2
  • 15
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • DOI 10.1038/35103511
    • Eddy, S.R. 2001. Noncoding RNA genes and the modern RNA world. Nat. Rev. Genet. 2, 919-929. (Pubitemid 33691089)
    • (2001) Nature Reviews Genetics , vol.2 , Issue.12 , pp. 919-929
    • Eddy, S.R.1
  • 16
    • 39049095811 scopus 로고    scopus 로고
    • Eukaryotic gene prediction by spectral analysis and pattern recognition techniques
    • Eftestol, T., Ryen, T., Aase, S.O., et al. 2006. Eukaryotic gene prediction by spectral analysis and pattern recognition techniques. Proc. 7th Nordic Signal Process. Symp.
    • (2006) Proc. 7th Nordic Signal Process. Symp
    • Eftestol, T.1    Ryen, T.2    Aase, S.O.3
  • 18
    • 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
  • 19
    • 1542363555 scopus 로고    scopus 로고
    • A digital signal processing method for gene prediction with improved noise suppression
    • Fox, T., and Carreira, A. 2004. A digital signal processing method for gene prediction with improved noise suppression. EURASIP J. Appl. Signal. Process. 1, 108-114.
    • (2004) EURASIP J. Appl. Signal. Process. , vol.1 , pp. 108-114
    • Fox, T.1    Carreira, A.2
  • 20
    • 0346991453 scopus 로고    scopus 로고
    • The unseen genome: Beyond DNA
    • Gibbs, W.W. 2003. The unseen genome: beyond DNA. Sci. Am. 108-113.
    • (2003) Sci. Am. , pp. 108-113
    • Gibbs, W.W.1
  • 22
    • 39349097702 scopus 로고    scopus 로고
    • Boosting approach to exon detection in DNA sequences
    • DOI 10.1049/el:20082343
    • Gunawan, T., Epps, J., and Ambikairajah, E. 2008. Boosting approach to exon detection in DNA sequences. Electron Lett. 44, 323-324. (Pubitemid 351263194)
    • (2008) Electronics Letters , vol.44 , Issue.4 , pp. 323-324
    • Gunawan, T.S.1    Epps, J.2    Ambikairajah, E.3
  • 23
    • 63049104302 scopus 로고    scopus 로고
    • DSP technique for gene and exon prediction taking complex indicator sequence
    • Hota, M.K., and Srivastava, V.K. 2008. DSP technique for gene and exon prediction taking complex indicator sequence. Proc. IEEE TENCON 2008.
    • (2008) Proc. IEEE TENCON 2008
    • Hota, M.K.1    Srivastava, V.K.2
  • 24
    • 57149120570 scopus 로고    scopus 로고
    • Coding region prediction based on a universal DNA sequence representation method
    • Jiang, X., Lavenier, D., and Yau, S. 2008. Coding region prediction based on a universal DNA sequence representation method. J. Comput. Biol. 15, 1237-1256.
    • (2008) J. Comput. Biol. , vol.15 , pp. 1237-1256
    • Jiang, X.1    Lavenier, D.2    Yau, S.3
  • 25
    • 51749095041 scopus 로고    scopus 로고
    • Prediction of protein-coding regions in DNA sequences using a model-based approach
    • Kahumani, R., Devabhaktuni, V., and Ahmad, M. 2008. Prediction of protein-coding regions in DNA sequences using a model-based approach. Proc. IEEE Int. Symp. Circuits Syst. 1918-1921.
    • (2008) Proc. IEEE Int. Symp. Circuits Syst. , pp. 1918-1921
    • Kahumani, R.1    Devabhaktuni, V.2    Ahmad, M.3
  • 26
    • 0042525755 scopus 로고    scopus 로고
    • Gene prediction by spectral rotation measure: A new method for identifying protein-coding regions
    • Kotlar, D., and Lavner, Y. 2003. Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions. Genome Res. 13, 1930-1937. (Pubitemid 36987200)
    • (2003) Genome Research , vol.13 , Issue.8 , pp. 1930-1937
    • Kotlar, D.1    Lavner, Y.2
  • 27
    • 0030623944 scopus 로고    scopus 로고
    • Two methods for improving performance of an HMM and their applications for gene-finding
    • Krogh, A. 1997. Two methods for improving performance of an HMM and their applications for gene-finding. Proc. 5th Int. Conf. Intell. Syst. Mol. Biol. 179-186.
    • (1997) Proc. 5th Int. Conf. Intell. Syst. Mol. Biol. , pp. 179-186
    • Krogh, A.1
  • 28
    • 37649027056 scopus 로고    scopus 로고
    • Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome
    • Li, W., and Holste, D. 2005. Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome. Phys. Rev. E 71, 041910.
    • (2005) Phys. Rev. e , vol.71 , pp. 041910
    • Li, W.1    Holste, D.2
  • 29
    • 24044536613 scopus 로고    scopus 로고
    • Pattern recognition techniques for the emerging field of bioinformatics: A review
    • DOI 10.1016/j.patcog.2005.02.019, PII S0031320305001263
    • Liew, A., Yan, H., and Yang, M. 2005. Pattern recognition techniques for the emerging field of bioinformatics: a review. Pattern Recogn. 38, 2055-2073. (Pubitemid 41214645)
    • (2005) Pattern Recognition , vol.38 , Issue.11 , pp. 2055-2073
    • Liew, A.W.-C.1    Yan, H.2    Yang, M.3
  • 33
    • 0036596123 scopus 로고    scopus 로고
    • Computer programs for eukaryotic gene prediction
    • Makarov, V. 2002. Computer programs for eukaryotic gene prediction. Brief Bioinform. 3, 195-199.
    • (2002) Brief Bioinform. , vol.3 , pp. 195-199
    • Makarov, V.1
  • 34
    • 77955919712 scopus 로고    scopus 로고
    • Theoretical justification of computing the 3-base periodicity using nucleotide distribution variance
    • doi:10.1016/j.biosystems.2010.07.001
    • Marhon, S., and Kremer, S.C. 2010. Theoretical justification of computing the 3-base periodicity using nucleotide distribution variance. BioSystems. doi:10.1016/j.biosystems.2010.07.001.
    • (2010) BioSystems
    • Marhon, S.1    Kremer, S.C.2
  • 35
    • 43849083883 scopus 로고    scopus 로고
    • Identification of protein coding regions using the modified Gabor-Wavelet transform
    • Mena-Chalco, J., Carrer, H., Zana, Y., et al. 2008. Identification of protein coding regions using the modified Gabor-Wavelet transform. IEEE ACM Trans. Comput. Biol. 5, 198-207.
    • (2008) IEEE ACM Trans. Comput. Biol. , vol.5 , pp. 198-207
    • Mena-Chalco, J.1    Carrer, H.2    Zana, Y.3
  • 36
    • 0000347441 scopus 로고
    • A new graphical representation and analysis of DNAc sequence structure: Methodology and application to globin genes
    • Nandy, A. 1994. A new graphical representation and analysis of DNAc sequence structure: methodology and application to globin genes. Curr. Sci. 66, 309-314.
    • (1994) Curr. Sci. , vol.66 , pp. 309-314
    • Nandy, A.1
  • 37
    • 79957517062 scopus 로고    scopus 로고
    • George Gamow and the genetic code
    • Nanjundiah, V. 2004. George Gamow and the genetic code. Resonance 9, 44-49.
    • (2004) Resonance , vol.9 , pp. 44-49
    • Nanjundiah, V.1
  • 38
    • 69149109819 scopus 로고    scopus 로고
    • A novel ACO-GA hybrid algorithm for feature selection in protein function prediction
    • Nemati, S., Basiri, M., Ghasem-Aghaee, N., et al. 2009. A novel ACO-GA hybrid algorithm for feature selection in protein function prediction. Expert Syst. Appl. 36, 12086-12094.
    • (2009) Expert Syst. Appl. , vol.36 , pp. 12086-12094
    • Nemati, S.1    Basiri, M.2    Ghasem-Aghaee, N.3
  • 39
    • 0035002807 scopus 로고    scopus 로고
    • Evaluation of gene-finding programs on mammalian sequences
    • DOI 10.1101/gr.147901
    • Rogic, S., Mackworth, A.K., and Ouellette, B.F. 2001. Evaluation of gene finding programs on mammalian sequences. Genome Res. 11, 817-832. (Pubitemid 32447866)
    • (2001) Genome Research , vol.11 , Issue.5 , pp. 817-832
    • Rogic, S.1    Mackworth, A.K.2    Ouellette, F.B.F.3
  • 40
    • 33847329566 scopus 로고    scopus 로고
    • In search of the small ones: Improved prediction of short exons in vertebrates, plants, fungi and protists
    • DOI 10.1093/bioinformatics/btl639
    • Saeys, Y., Rouze, P., and de Peer, Y.V. 2007. In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinformatics 23, 414-420. (Pubitemid 46323121)
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 414-420
    • Saeys, Y.1    Rouze, P.2    Van De Peer, Y.3
  • 42
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNAs
    • Storz, C. 2002. An expanding universe of noncoding RNAs. Science 296, 1260-1263.
    • (2002) Science , vol.296 , pp. 1260-1263
    • Storz, C.1
  • 45
    • 0025833642 scopus 로고
    • Periodicity in DNA coding sequences: Implications in gene evolution
    • Tsonis, A., Elsner, J., and Tsonis, P. 1991. Periodicity in DNA coding sequences: implications in gene evolution. J. Theor. Biol. 151, 323-331.
    • (1991) J. Theor. Biol. , vol.151 , pp. 323-331
    • Tsonis, A.1    Elsner, J.2    Tsonis, P.3
  • 47
    • 0000204878 scopus 로고
    • Evolution of long-range fractal correlations and 1/f noise in DNA base sequences
    • Voss, R.F. 1992. Evolution of long-range fractal correlations and 1/f noise in DNA base sequences. Phys. Rev. Lett. 68, 3805-3808.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 3805-3808
    • Voss, R.F.1
  • 49
    • 0031760475 scopus 로고    scopus 로고
    • A new Fourier transform approach for protein coding measure based on the format of the Z curve
    • DOI 10.1093/bioinformatics/14.8.685
    • Yan, M., Lin, Z.S., and Zhang, C.T. 1998. A new Fourier transform approach for protein coding measure based on the format Z-curve. Bioinformatics 14, 685-690. (Pubitemid 28504993)
    • (1998) Bioinformatics , vol.14 , Issue.8 , pp. 685-690
    • Yan, M.1    Lin, Z.-S.2    Zhang, C.-T.3
  • 51
    • 28744458836 scopus 로고    scopus 로고
    • A Fourier characteristic of coding sequences: Origins and a non-Fourier approximation
    • DOI 10.1089/cmb.2005.12.1153
    • Yin, C., and Yau, S. 2005. A Fourier characteristics of coding sequences: origins and a non-Fourier approximation. J. Comput. Biol. 12, 1153-1165. (Pubitemid 41759887)
    • (2005) Journal of Computational Biology , vol.12 , Issue.9 , pp. 1153-1165
    • Yin, C.1    Yau, S.S.-T.2
  • 52
    • 34447542501 scopus 로고    scopus 로고
    • Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence
    • DOI 10.1016/j.jtbi.2007.03.038, PII S0022519307001543
    • Yin, C., and Yau, S. 2007. Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence. J. Theor. Biol. 247, 687-694. (Pubitemid 47081038)
    • (2007) Journal of Theoretical Biology , vol.247 , Issue.4 , pp. 687-694
    • Yin, C.1    Yau, S.S.-T.2
  • 53
    • 65449167165 scopus 로고    scopus 로고
    • DV-Curve: A novel intuitive tool for visualizing and analyzing DNA sequences
    • Zhang, Z. 2009. DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences. Bioinformatics 25, 1112-1117.
    • (2009) Bioinformatics , vol.25 , pp. 1112-1117
    • Zhang, Z.1
  • 54
    • 0027995001 scopus 로고
    • Z curves, an intutive tool for visualizing and analyzing the DNA sequences
    • Zhang, R., and Zhang, C.T. 1994. Z curves, an intuitive tool for visualizing and analyzing the DNA sequences. J. Biomol. Struct. Dyn. 11, 767-782. (Pubitemid 24089977)
    • (1994) Journal of Biomolecular Structure and Dynamics , vol.11 , Issue.4 , pp. 767-782
    • Zhang, R.1    Zhang, C.-T.2
  • 55
    • 49749128373 scopus 로고    scopus 로고
    • Time-frequency analysis of click-evoked otoacoustic emissions by means of a minimum variance spectral estimation-based method
    • Zhang, Z.G., Zhang, V.W., Chan S.C., et al. 2008. Time-frequency analysis of click-evoked otoacoustic emissions by means of a minimum variance spectral estimation-based method. Hearing Res. 243, 18-27.
    • (2008) Hearing Res. , vol.243 , pp. 18-27
    • Zhang, Z.G.1    Zhang, V.W.2    Chan, S.C.3


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