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Volumn 13, Issue 5, 2009, Pages 747-755

Detection of tandem repeats in DNA sequences based on parametric spectral estimation

Author keywords

Autoregressive (AR) model; DNA sequence analysis; Spectral analysis; Tandem repeats

Indexed keywords

AUTO REGRESSIVE MODELS; AUTOREGRESSIVE (AR) MODEL; DNA SEQUENCE ANALYSIS; EFFICIENT ALGORITHM; OTHER ALGORITHMS; REGULATORY FUNCTIONS; SPECTRAL ANALYSIS; SPECTRAL ESTIMATION; SPECTROGRAMS; TANDEM REPEATS;

EID: 70349414490     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2008.920626     Document Type: Article
Times cited : (27)

References (53)
  • 1
    • 70349411247 scopus 로고    scopus 로고
    • Online, Available
    • Molecular Biology Web Book. (2007). [Online]. Available: http:// www.web-books.com/MoBio/
    • (2007) Molecular Biology Web Book
  • 2
    • 56049094738 scopus 로고    scopus 로고
    • New York: Garland
    • T. A. Brown, Genomes 3. New York: Garland, 2007, pp. 216-219.
    • (2007) Genomes 3 , pp. 216-219
    • Brown, T.A.1
  • 4
    • 8844283350 scopus 로고    scopus 로고
    • Exhaustive whole-genome tandem repeats search
    • A. Krishnan and F. Tang, "Exhaustive whole-genome tandem repeats search," Bioinformatics, vol. 20, no. 16, pp. 2702-2710, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2702-2710
    • Krishnan, A.1    Tang, F.2
  • 5
    • 33750078973 scopus 로고    scopus 로고
    • Search and classification of potential minisatellite sequences from bacterial genomes
    • A. Shelenkov, K. Skryabin, and E. Korotkov, "Search and classification of potential minisatellite sequences from bacterial genomes," DNA Res., vol. 13, no. 3, pp. 89-102, 2006.
    • (2006) DNA Res , vol.13 , Issue.3 , pp. 89-102
    • Shelenkov, A.1    Skryabin, K.2    Korotkov, E.3
  • 6
    • 0006886838 scopus 로고
    • Linear time recognition of square free strings
    • Combinatorial Algorithms on Words , New York: Springer-Verlag
    • M. G. Main and R. J. Lorentz, "Linear time recognition of square free strings," Combinatorial Algorithms on Words (NATO ASI Series, Series F: Computer and System Sciences). New York: Springer-Verlag, vol. 12, pp. 272-278, 1985.
    • (1985) NATO ASI Series, Series F: Computer and System Sciences , vol.12 , pp. 272-278
    • Main, M.G.1    Lorentz, R.J.2
  • 7
    • 0035999989 scopus 로고    scopus 로고
    • TROLL - Tandem repeat occurrence locator
    • A. T. Castelo, W. Martins, and G. R. Gao, "TROLL - Tandem repeat occurrence locator," Bioinformatics, vol. 18, no. 4, pp. 634-636, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.4 , pp. 634-636
    • Castelo, A.T.1    Martins, W.2    Gao, G.R.3
  • 8
    • 0038278603 scopus 로고    scopus 로고
    • An exhaustive DNA micro-satellite map of the human genome using high performance computing
    • J. R. Collins, R. M. Stephens, B. Gold, B. Long, M. Dean, and S. K. Burt, "An exhaustive DNA micro-satellite map of the human genome using high performance computing," Genomics, vol. 82, no. 1, pp. 10-19, 2003.
    • (2003) Genomics , vol.82 , Issue.1 , pp. 10-19
    • Collins, J.R.1    Stephens, R.M.2    Gold, B.3    Long, B.4    Dean, M.5    Burt, S.K.6
  • 9
    • 84943246104 scopus 로고    scopus 로고
    • Finding approximate repetitions under Hamming distance
    • Proc. ESA: Annu. Eur. Symp. Algorithms
    • R. Kolpakov and K. Gregory, "Finding approximate repetitions under Hamming distance," in Proc. ESA: Annu. Eur. Symp. Algorithms (Lecture Notes in Computer Science), 2001, vol. 2161, pp. 170-181.
    • (2001) Lecture Notes in Computer Science , vol.2161 , pp. 170-181
    • Kolpakov, R.1    Gregory, K.2
  • 10
    • 0004484243 scopus 로고    scopus 로고
    • An algorithm for locating nonoverlapping regions of maximum alignment score
    • S. K. Kannan and E.W. Myers, "An algorithm for locating nonoverlapping regions of maximum alignment score," SIAM J. Comput., vol. 25, no. 3, pp. 648-662, 1996.
    • (1996) SIAM J. Comput , vol.25 , Issue.3 , pp. 648-662
    • Kannan, S.K.1    Myers, E.W.2
  • 11
    • 0004511957 scopus 로고
    • A space-efficient algorithm for finding best scoring nonoverlapping alignments
    • G. Benson, "A space-efficient algorithm for finding best scoring nonoverlapping alignments," Theor. Comput. Sci., vol. 145, no. 1/2, pp. 357-369, 1995.
    • (1995) Theor. Comput. Sci , vol.145 , Issue.1-2 , pp. 357-369
    • Benson, G.1
  • 12
    • 0031674761 scopus 로고    scopus 로고
    • Identifying satellites in nucleic acid sequences
    • S. Istrail, P. Pevzner, and M.Waterman, Eds. New York: ACM
    • M.-F. Sagot and E. W. Myers, "Identifying satellites in nucleic acid sequences," in Proc. 2nd Annu. Int. Conf. Res. Comput. Mol. Biol. (RECOMB 1998), S. Istrail, P. Pevzner, and M.Waterman, Eds. New York: ACM, 1998, pp. 234-242.
    • (1998) Proc. 2nd Annu. Int. Conf. Res. Comput. Mol. Biol. (RECOMB 1998) , pp. 234-242
    • Sagot, M.-F.1    Myers, E.W.2
  • 13
    • 8844283350 scopus 로고    scopus 로고
    • Exhaustive whole-genome tandem repeats search
    • A. Krishnan and F. Tang, "Exhaustive whole-genome tandem repeats search," Bioinformatics, vol. 20, no. 16, pp. 2702-2710, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2702-2710
    • Krishnan, A.1    Tang, F.2
  • 15
    • 33846664609 scopus 로고    scopus 로고
    • Tandem repeats over the edit distance
    • D. Sokol, G. Benson, and J. Tojeira, "Tandem repeats over the edit distance," Bioinformatics, vol. 23, no. 2, pp. e30-e35, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.2
    • Sokol, D.1    Benson, G.2    Tojeira, J.3
  • 16
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • G. Benson, "Tandem repeats finder: A program to analyze DNA sequences," Nucleic Acids Res., vol. 27, no. 2, pp. 573-580, 1999.
    • (1999) Nucleic Acids Res , vol.27 , Issue.2 , pp. 573-580
    • Benson, G.1
  • 18
    • 8844220452 scopus 로고    scopus 로고
    • STAR: An algorithm to search for tandem approximate repeats
    • O. Delgrange and E. Rivals, "STAR: An algorithm to search for tandem approximate repeats," Bioinformatics, vol. 20, no. 16, pp. 2812-2820, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2812-2820
    • Delgrange, O.1    Rivals, E.2
  • 20
    • 18244405741 scopus 로고    scopus 로고
    • Evaluation of the color-coding method for searching tandem repeats in prokaryotic genomes
    • S. Mizuta, H. Munakata, A. Aimaiti, K. Oosawa, and T. Shimizu, "Evaluation of the color-coding method for searching tandem repeats in prokaryotic genomes," Chem. Bio. Inf. J., vol. 4, no. 4, pp. 133-141, 2004.
    • (2004) Chem. Bio. Inf. J , vol.4 , Issue.4 , pp. 133-141
    • Mizuta, S.1    Munakata, H.2    Aimaiti, A.3    Oosawa, K.4    Shimizu, T.5
  • 21
    • 0030825816 scopus 로고    scopus 로고
    • Residual colours: A proposal for aminochromography
    • W. R. Taylor, "Residual colours: A proposal for aminochromography," Protein Eng., vol. 10, no. 7, pp. 743-746, 1997.
    • (1997) Protein Eng , vol.10 , Issue.7 , pp. 743-746
    • Taylor, W.R.1
  • 22
    • 0034607545 scopus 로고    scopus 로고
    • Color-coding reveals tandem repeats in the Escherichia coli genome
    • T. Yoshida, N. Obata, and K. Oosawa, "Color-coding reveals tandem repeats in the Escherichia coli genome," J. Mol. Biol., vol. 298, no. 3, pp. 343-349, 2000.
    • (2000) J. Mol. Biol , vol.298 , Issue.3 , pp. 343-349
    • Yoshida, T.1    Obata, N.2    Oosawa, K.3
  • 24
    • 0034491149 scopus 로고    scopus 로고
    • Frequency-domain analysis of biomolecular sequence
    • D. Anastassiou, "Frequency-domain analysis of biomolecular sequence," Bioinformatics, vol. 16, no. 12, pp. 1073-1081, 2000.
    • (2000) Bioinformatics , vol.16 , Issue.12 , pp. 1073-1081
    • Anastassiou, D.1
  • 25
    • 85032750863 scopus 로고    scopus 로고
    • Genomic signal processing
    • Jul
    • D. Anastassiou, "Genomic signal processing," IEEE Signal Process. Mag., vol. 18, no. 4, pp. 8-20, Jul. 2001.
    • (2001) IEEE Signal Process. Mag , vol.18 , Issue.4 , pp. 8-20
    • Anastassiou, D.1
  • 26
    • 11444250228 scopus 로고    scopus 로고
    • Genomics and proteomics:ASignal processor's tour
    • Oct
    • P. P.Vaidyanathan, "Genomics and proteomics:ASignal processor's tour," IEEE Circuits Syst. Mag., vol. 4, no. 4, pp. 6-29, Oct. 2004.
    • (2004) IEEE Circuits Syst. Mag , vol.4 , Issue.4 , pp. 6-29
    • Vaidyanathan, P.P.1
  • 27
    • 0037399772 scopus 로고    scopus 로고
    • Large scale features in DNA genomic signals
    • P. D. Cristea, "Large scale features in DNA genomic signals," Signal Process., vol. 83, pp. 871-888, 2003.
    • (2003) Signal Process , vol.83 , pp. 871-888
    • Cristea, P.D.1
  • 28
    • 34047140505 scopus 로고    scopus 로고
    • OMWSA: Detection of DNA repeats using moving window spectral analysis
    • L.-P. Du, H.-X. Zhou, and H. Yan, "OMWSA: Detection of DNA repeats using moving window spectral analysis," Bioinformatics, vol. 23, no. 5, pp. 631-633, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 631-633
    • Du, L.-P.1    Zhou, H.-X.2    Yan, H.3
  • 30
    • 0036503714 scopus 로고    scopus 로고
    • Computing linear transforms of symbolic signal
    • Mar
    • W. Wang and D. H. Johnson, "Computing linear transforms of symbolic signal," 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
  • 31
    • 0029098929 scopus 로고
    • Search of hidden periodicities in DNA sequences
    • V. R. Chechetkin and A. Y. Turygin, "Search of hidden periodicities in DNA sequences," J. Theoretical Biol., vol. 175, pp. 477-497, 1995.
    • (1995) J. Theoretical Biol , vol.175 , pp. 477-497
    • Chechetkin, V.R.1    Turygin, A.Y.2
  • 33
    • 0642343790 scopus 로고    scopus 로고
    • Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis
    • A. Fukushima, T. Ikemura, T. Oshima, and H. Mori, "Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis," Genome Inf., vol. 13, pp. 21-29, 2002.
    • (2002) Genome Inf , vol.13 , pp. 21-29
    • Fukushima, A.1    Ikemura, T.2    Oshima, T.3    Mori, H.4
  • 34
    • 0031010292 scopus 로고    scopus 로고
    • Prediction of probable genes by Fourier analysis of genomic sequences
    • S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, and R. Ramaswamy, "Prediction of probable genes by Fourier analysis of genomic sequences," CABIOS, vol. 13, no. 3, pp. 263-270, 1997.
    • (1997) CABIOS , vol.13 , Issue.3 , pp. 263-270
    • Tiwari, S.1    Ramachandran, S.2    Bhattacharya, A.3    Bhattacharya, S.4    Ramaswamy, R.5
  • 35
    • 1542363555 scopus 로고    scopus 로고
    • A digital signal processing method for gene prediction with improved noise suppression
    • T. W. Fox and A. Carreira, "A digital signal processing method for gene prediction with improved noise suppression," EURASIP J. Appl. Signal Process., vol. 2004, no. 1, pp. 108-114, 2004.
    • (2004) EURASIP J. Appl. Signal Process , vol.2004 , Issue.1 , pp. 108-114
    • Fox, T.W.1    Carreira, A.2
  • 36
    • 1542742235 scopus 로고    scopus 로고
    • The role of signal-processing concepts in genomics and proteomics
    • P. P. Vaidyanathan and B.-J. Yoon, "The role of signal-processing concepts in genomics and proteomics," J. Franklin Inst., vol. 341, pp. 111-135, 2004.
    • (2004) J. Franklin Inst , vol.341 , pp. 111-135
    • Vaidyanathan, P.P.1    Yoon, B.-J.2
  • 38
    • 4544370695 scopus 로고    scopus 로고
    • Techniques for detecting approximate tandem repeats in DNA
    • Speech Signal Process, ICASSP, May, pp
    • T. T. Tran, V. A. Emanuele, II, and G.-T. Zhou, "Techniques for detecting approximate tandem repeats in DNA," in Proc. IEEE Int. Conf. Acoust., Speech Signal Process. (ICASSP 2004), vol. 5, May, pp. 449-452.
    • (2004) Proc. IEEE Int. Conf. Acoust , vol.5 , pp. 449-452
    • Tran, T.T.1    Emanuele II, V.A.2    Zhou, G.-T.3
  • 40
    • 3142727129 scopus 로고    scopus 로고
    • Spectral repeat finder (SRF): Identification of repetitive sequences using Fourier transformation
    • D. Sharma, B. Issac, G. P. S. Raghava, and R. Ramaswamy, "Spectral repeat finder (SRF): Identification of repetitive sequences using Fourier transformation," Bioinformatics, vol. 20, no. 9, pp. 1405-1412, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1405-1412
    • Sharma, D.1    Issac, B.2    Raghava, G.P.S.3    Ramaswamy, R.4
  • 41
    • 0042411993 scopus 로고    scopus 로고
    • Detection and visualization of tandem repeats in DNA sequences
    • Sep
    • M. Buchner and S. Janjarasjitt, "Detection and visualization of tandem repeats in DNA sequences," IEEE Trans. Signal Process., vol. 51, no. 9, pp. 2280-2287, Sep. 2003.
    • (2003) IEEE Trans. Signal Process , vol.51 , Issue.9 , pp. 2280-2287
    • Buchner, M.1    Janjarasjitt, S.2
  • 42
    • 34247236699 scopus 로고    scopus 로고
    • A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences
    • R. Gupta, D. Sarthi, A. Mittal, and K. Singh, "A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences," EURASIP J. Bioinf. Syst. Biol., vol. 2007, pp. 1-8, 2007.
    • (2007) EURASIP J. Bioinf. Syst. Biol , vol.2007 , pp. 1-8
    • Gupta, R.1    Sarthi, D.2    Mittal, A.3    Singh, K.4
  • 43
    • 0019636227 scopus 로고
    • Spectrum analysis - Amodern perspective
    • Nov
    • S. M. Kay and S. L. Marple, "Spectrum analysis - Amodern perspective," Proc. IEEE, vol. 69, no. 11, pp. 1380-1419, Nov. 1981.
    • (1981) Proc. IEEE , vol.69 , Issue.11 , pp. 1380-1419
    • Kay, S.M.1    Marple, S.L.2
  • 45
    • 0037297977 scopus 로고    scopus 로고
    • Adaptive, autoregressive spectral estimation for analysis of electrical signals of gastric origin
    • E. R. Moraes, L. E. A. Troncon, O. Baffa, A. S. Oba-Kunyioshi, R.Wakai, andA. Leuthold, "Adaptive, autoregressive spectral estimation for analysis of electrical signals of gastric origin," Physiol. Meas. vol. 24, no. 1, pp. 91-106, 2003.
    • (2003) Physiol. Meas , vol.24 , Issue.1 , pp. 91-106
    • Moraes, E.R.1    Troncon, L.E.A.2    Baffa, O.3    Oba-Kunyioshi, A.S.4    Wakai, R.5    andA6    Leuthold7
  • 47
    • 31444447435 scopus 로고    scopus 로고
    • Tutorial on univariate autoregressive spectral analysis
    • R. Takalo, H. Hytti, and H. Ihalainen, "Tutorial on univariate autoregressive spectral analysis," J. Clin. Monitoring Comput., vol. 19, no. 6, pp. 401-410, 2005.
    • (2005) J. Clin. Monitoring Comput , vol.19 , Issue.6 , pp. 401-410
    • Takalo, R.1    Hytti, H.2    Ihalainen, H.3
  • 48
    • 0032124011 scopus 로고    scopus 로고
    • Autoregressive model order selection by a finite sample estimator for the Kullback-Leibler discrepancy
    • Jul
    • P. M. T. Broersen and H. E. Wensink, "Autoregressive model order selection by a finite sample estimator for the Kullback-Leibler discrepancy," IEEE Trans. Signal Process., vol. 46, no. 7, pp. 2058-2061, Jul. 1998.
    • (1998) IEEE Trans. Signal Process , vol.46 , Issue.7 , pp. 2058-2061
    • Broersen, P.M.T.1    Wensink, H.E.2
  • 49
    • 2942605849 scopus 로고    scopus 로고
    • Finite sample properties of ARMA order selection
    • Jun
    • P. M. T. Broersen and S. de Waele, "Finite sample properties of ARMA order selection," IEEE Trans. Instrum. Meas., vol. 53, no. 3, pp. 645-651, Jun. 2004.
    • (2004) IEEE Trans. Instrum. Meas , vol.53 , Issue.3 , pp. 645-651
    • Broersen, P.M.T.1    de Waele, S.2
  • 50
    • 85033517914 scopus 로고
    • A Bayesian extension of the minimum AIC procedure of autoregressive model fitting
    • H. Akaike, "A Bayesian extension of the minimum AIC procedure of autoregressive model fitting," Biometrika, vol. 66, no. 2, pp. 237-242, 1979.
    • (1979) Biometrika , vol.66 , Issue.2 , pp. 237-242
    • Akaike, H.1
  • 53
    • 85142187953 scopus 로고    scopus 로고
    • V. Boeva, M. Regnier,D. Papatsenko, andV. Makeev, Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression, Bioinformatics, 22, no. 6, pp. 676-684, 2006.
    • V. Boeva, M. Regnier,D. Papatsenko, andV. Makeev, "Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression," Bioinformatics, vol. 22, no. 6, pp. 676-684, 2006.


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