Sequential modeling for identifying CpG island locations in human genome

IEEE Signal Processing Letters

Volumn 9, Issue 12, 2002, Pages 407-409

  Dasgupta, Nilanjan ^a   Lin, Simon ^b   Carin, Lawrence ^a  

^a Duke University   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

DNA; Genes; HMM; Markov models

Indexed keywords

DNA SEQUENCES; FIR FILTERS; GENETIC ALGORITHMS; MARKOV PROCESSES; MATHEMATICAL MODELS; OPTIMIZATION; STATISTICAL METHODS; TIME DOMAIN ANALYSIS; TREES (MATHEMATICS); WAVELET TRANSFORMS;

HIDDEN MARKOV MODEL; HIDDEN MARKOV TREE; SEQUENTIAL PROCESSING ALGORITHMS;

SIGNAL ENCODING;

EID: 0036963612     PISSN: 10709908     EISSN: None     Source Type: Journal    
DOI: 10.1109/LSP.2002.806062     Document Type: Letter

References (16)

1. T. A. Brown, Genomes. New York: Wiley, 1999.
2. D. R. Cox and H. D. Miller, The Theory of Stochastic Processes. London, U.K.: Chapman & Hall, 1965.
3. A. C. Camproux et al., "Hidden Markov model approach for identifying the molecular framework of the protein backbone," Protein Eng., vol. 12, no. 12, pp. 1063-1073, Dec. 1999.
4. L. R. Rabiner and B. H. Juang, "An introduction to hidden Markov models," IEEE Acoust., Speech, Signal Processing Mag., vol. 3, pp. 4-16, Jan. 1986.
5. M. S. Crouse, R. D. Nowak, and R. G. Baraniuk, "Wavelet-based statistical signal processing using hidden Markov models," IEEE Trans. Signal Processing, vol. 46, pp. 886-902, Apr. 1998.
6. R. Hughley and A. Krogh, "Hidden Markov models for sequence analysis: Extension and analysis of the basic method," Comput. Appl. Biosci., vol. 12, pp. 95-107.
7. D. Anastassiou, "Frequency-domain analysis of biomolecular sequences," Bioinformatics, vol. 16, no. 12, pp. 1073-1081, 2000.
8. W. Sweldens, "The lifting scheme: A custom-design construction of biorthogonal wavelets," J. Appl. Comput. Harmon. Anal., vol. 3, pp. 186-200, 1996.
9. E. Jones, P. Runkle, N. Dasgupta, L. Couchman, and L. Carin, "Genetic algorithm wavelet design for signal classification," IEEE Pattern Anal. Mach. Intell., vol. 23, pp. 890-895, Aug. 2001.
10. Sanger Institute. (2002). [Online]. Available: ftp://ftp.sanger.ac.uk/pub/human/sequences/CpG_Island_tag_sequences/CpG_island_ library_reads
11. NIH. (2002). GenBank. [Online]. Available: http://www.ncbi.nlm.nih.gov
12. I. Daubechies, "Ten lectures on wavelets," CBMS-NSF Lecture Notes, vol. 61, 1992.
13. C. S. Burrus, R. A. Gopinath, and H. Guo, Introduction to Wavelets and Wavelet Transforms. Englewood Cliffs, NJ: Prentice-Hall, 1998.
14. J. P. Fitch and B. Sokhansanj, "Genomic engineering: Moving beyond DNA sequence to function," Proc. IEEE, vol. 88, Dec. 2000.
15. R. L. Claypoole, R. G. Baraniuk, and R. D. Nowak, "Adaptive wavelet transforms via lifting," in Proc. ICASSP, 1998.
16. N. Dasgupta, P. Runkle, L. Couchman, and L. Carin, "Dual hidden Markov model for characterizing wavelet coefficients from multi-aspect scattering data," Signal Process., May 2001.