Optimal structure for automatic processing of DNA sequences

IEEE Transactions on Biomedical Engineering

Volumn 46, Issue 9, 1999, Pages 1044-1056

  Davies, Stephen W ^a   Eizenman, Moshe ^a   Pasupathy, Subbarayan ^a  

^a LUCENT TECHNOLOGIES   (United States)

Author keywords

DNA modeling; DNA sequencing; Maximum likelihood sequence detection (MLSD); Nuisance parameters; Timing jitter

Indexed keywords

ALGORITHMS; BIOMEDICAL ENGINEERING; MATHEMATICAL MODELS; MAXIMUM LIKELIHOOD ESTIMATION; MOLECULAR STRUCTURE; PARAMETER ESTIMATION; TIME SERIES ANALYSIS;

MAXIMUM-LIKELIHOOD SEQUENCE DETECTION (MLSD);

DNA SEQUENCES;

DNA;

ALGORITHM; ARTICLE; AUTOMATION; DNA SEQUENCE; DNA TEMPLATE; ELECTROPHORESIS; MAXIMUM LIKELIHOOD METHOD;

ALGORITHMS; ANIMALS; ELECTROPHORESIS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; LENS, CRYSTALLINE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 0032869848     PISSN: 00189294     EISSN: None     Source Type: Journal    
DOI: 10.1109/10.784135     Document Type: Article

References (24)

1. T. A. Brown, DNA Sequencing: The Basics, Oxford University Press, New York, 1994.
2. Y. Xu, R. J. Mural, and E. C. Uberbacher, "Correcting sequencing errors in DNA coding regions using a dynamic programming approach," Computer Applications in Biosciences, vol. 11, no. 2, pp. 117-124, 1995.
3. Y. Wu and D. Mislan, "Automated DNA sequencing: An image processing approach," Appl. Theoretical Electrophoresis, vol. 3, pp. 223-228, 1993.
4. A. J. Berno, "A graph theoretic approach to the analysis of DNA sequencing data," Genome Res., vol. 6, no. 2, pp. 80-91, 1996.
5. M. Giddings, R. Brumley, M. Haker, and L. Smith, "An adaptive, objectoriented strategy for base calling in DNA sequencing analysis," Nucleic Acids Res., vol. 21, no. 19, pp. 4530-4540, 1993.
6. J. Ives, R. Gesteland, and T. Stockham, "An automated film reader for DNA sequencing based on homomorphic deconvolution," IEEE Trans. Biomed. Eng., vol. 41, pp. 509-519, June 1994.
7. C. Tibbetts and J. Bowling, "Method and apparatus for automatic nucleic acid sequence determination," US Patent no. 5365455, Nov. 15, 1994.
8. C. Tibbetts, J. Bowling, and J. Golden, "Neural networks for automated basecalling of gel-based DNA sequencing ladders," in Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and J. Venter, Eds.. New York: Academic, 1994, pp. 219-229.
9. J. Bowling, K. Bruner, J. Cmarik, and C. Tibbets, "Neighboring nucleotide interactions during DNA sequencing gel electrophoresis," Nucleic Acids Res., vol. 19, no. 11, pp. 3089-3097, 1991.
10. E. Lee and D. Messerschchmitt, Digital Communication, 2nd ed. New York: Kluwer, 1994.
11. J. G. Proakis, Digital Communications, 3rd ed. New York: McGraw Hill, 1995.
12. H. Van Trees, Detection, Estimation and Modulation Theory. New York: Wiley, 1968.
13. D. Falconer and J. Salz, "Optimal reception of digital data over the Gaussian channel with unknown delay and phase jitter," IEEE Trans. Inform. Theory, vol. 23, pp. 117-126, Jan. 1977.
14. C. Georghiades, "Optimal delay and sequence estimation from incomplete data," IEEE Trans. Inform. Theory, vol. 36, pp. 202-208, Jan. 1990.
15. M. Moeneclaey, "Synchronization problems in PAM systems," IEEE Trans. Commun., vol. 28, pp. 1130-1136, Aug. 1980.
16. J. B. Anderson and S. Mohan, "Sequential coding algorithms: A survey and cost analysis," IEEE Trans. Commun., vol. C-32, pp. 169-176, Feb. 1984.
17. S. W. Davies, M. Eizenman, and S. Pasupathy, "Exploiting multichannel information in systems with high symbol clock variance," in Proc. Canadian Workshop on Information Theory, Toronto, Canada, June 1997, pp. 91-94.
18. X. Yu and S. Pasupathy, "Innovations-based MLSE for Rayleigh fading channels," IEEE Trans. Commun., vol. 43, pp. 1534-1544, Feb./Mar./Apr. 1995.
19. P. R. Kumar and P. Varaiya, Stochastic Systems: Estimation, Identification and Adaptive Control. Englewood Cliffs, NJ: Prentice-Hall, 1986.
20. T. Aulin, "Breadth first maximum-likelihood sequence detection," submitted for publication
21. J. H. Lodge and M. L. Moher, "Maximum-likelihood sequence estimation of CPM signals transmitted over Rayleigh flat-fading channels," IEEE Trans. Commun., vol. 38, pp. 787-794, June 1990.
22. G. J. Caspers, J. Pennings, and W. W. de Jong, "A partial cDNA sequence corrects the human alpha A crystalline primary structure," Exp. Eye Res., vol. 59, pp. 125-126, 1994.
23. G. Slater, personal communication.
24. H.-G. Elias, An Introduction to Polymer Science. Weinheim, Germany: VCH, 1997.