A Digital Signal Processing Method for Gene Prediction with Improved Noise Suppression

Eurasip Journal on Applied Signal Processing

Volumn 2004, Issue 1, 2004, Pages 108-114

  Fox, Trevor W ^a   Carreira, Alex ^b  

^a Intelligent Engines   (Canada)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

Digital filter; DNA; Gene prediction

Indexed keywords

BIOSYNTHESIS; COMPUTERS; DATA REDUCTION; DIGITAL FILTERS; DISCRETE FOURIER TRANSFORMS; DNA SEQUENCES; GENES; SIGNAL TO NOISE RATIO;

CODING REGIONS; GENE PREDICTION; PROTEIN CODING;

DIGITAL SIGNAL PROCESSING;

EID: 1542363555     PISSN: 11108657     EISSN: None     Source Type: Journal    
DOI: 10.1155/S1110865704309285     Document Type: Article

References (21)

1. D. Anastassiou, "Genomic signal processing," IEEE Signal Processing Magazine, vol. 18, no. 4, pp. 8-20, 2001.
2. P. P. Vaidyanathan and B.-J. Yoon, "Digital filters for gene prediction applications," in Proc. Asilomar Conference on Signals, Systems, and Computers, pp. 306-310, Pacific Grove, Calif, USA, November 2002.
3. D. Anastassiou, "DSP in genomics," in Proc. IEEE Int. Conf. Acoustics, Speech, Signal Processing, pp. 1053-1056, Salt Lake City, Utah, USA, May 2001.
4. S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, and R. Ramaswamy, "Prediction of probable genes by Fourier analysis of genomic sequences," Comput. Appl. Biosci., vol. 13, no. 3, pp. 263-270, 1997.
5. J. W. Fickett, "Recognition of protein coding regions in DNA sequences," Nucleic Acids Res., vol. 10, no. 17, pp. 5303-5318, 1982.
6. P. P. Vaidyanathan and B.-J. Yoon, "Gene and exon prediction using allpass-based filters," in Workshop on Genomic Signal Processing and Statistics, Raleigh, NC, USA, October 2002.
7. J. Henderson, S. Salzberg, and K. H. Fasman, "Finding genes in DNA with a hidden Markov model," J. Comput Biol., vol. 4, no. 2, pp. 127-141, 1997.
8. D. Kulp, D. Haussler, M. G. Reese, and F. H. Eeckman, "A generalized hidden Markov model for the recognition of human genes in DNA, " in Proc. of the 4th International Conference on Intelligent Systems for Molecular Biology, Menlo Park, Calif, USA, 1996.
9. A. Krogh, I. S. Mian, and D. Haussler, "A hidden Markov model that finds genes in E. coli DNA," Nucleic Acids Res., vol. 22, no. 22, pp. 4768-4778, 1994.
10. C. B. Burge and S. Karlin, "Finding the genes in genomic DNA," Curr. Opin. Struct. Biol., vol. 8, no. 3, pp. 346-354, 1998.
11. P. D. Cristea, "Large scale features in DNA genomic signals," Signal Processing, vol. 83, no. 4, pp. 871-888, 2003.
12. W. Li, P. Bernaola-Galvan, F. Haghighi, and I. Grosse, "Applications of recursive segmentation to the analysis of DNA sequences," Computers & Chemistry, vol. 26, no. 5, pp. 491-510, 2002.
13. W. Li, G. Stolovitzky, P. Bernaola-Galvan, and J. L. Oliver, "Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes," Genome Research, vol. 8, no. 9, pp. 916-928, 1998.
14. A. Oppenheim and R. Schafer, Discrete-Time Signal Processing, Prentice-Hall, Englewood Cliffs, NJ, USA, 1989.
15. R. F. Voss, "Evolution of long-range fractal correlations and 1/f noise in DNA base sequences," Phys. Rev. Lett., vol. 68, no. 25, pp. 3805-3808, 1992.
16. W. Li, "The study of correlation structures of DNA sequences: a critical review," Computers & Chemistry, vol. 21, no. 4, pp. 257-271, 1997.
17. W. Li and K. Kaneko, "Long-range correlation and partial 1/f spectrum in a non-coding DNA sequence," Europhys. Lett., vol. 17, no. 7, pp. 655-660, 1992.
18. D. R. Forsdyke and J. R. Mortimer, "Chargaff's legacy," Gene, vol. 261, no. 1, pp. 127-137, 2000.
19. W. Li, "The study of correlation structures of DNA sequences: a critical review," Computers & Chemistry, vol. 21, no. 4, pp. 257-272, 1997.
20. J. W. Fickett, D. C. Torney, and D. R. Wolf, "Base compositional structure of genomes," Genomics, vol. 13, no. 4, pp. 1056-1064, 1992.
21. J. E. Dennis and R. B. Schnabel, Numerical Methods for Unconstrained Optimization and Nonlinear Equations, SIAM, Philadelphia, Pa, USA, 1996.