Bayesian basecalling for DNA sequence analysis using hidden Markov models

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 4, Issue 3, 2007, Pages 430-440

  Liang, Kuo Ching ^a   Wang, Xiaodong ^a   Anastassiou, Dimitris ^a  

^a Columbia University ^*

Author keywords

Basecalling; DNA sequencing; Electropherogram; Hidden Markov model (HMM); Markov chain Monte Carlo (MCMC)

Indexed keywords

BAYESIAN NETWORKS; COMPUTER SIMULATION; HIDDEN MARKOV MODELS; MONTE CARLO METHODS; VITERBI ALGORITHM;

BASECALLING; ELECTROPHEROGRAM; MARKOV CHAIN MONTE CARLO (MCMC);

DNA SEQUENCES;

LEGIONELLA PNEUMOPHILA;

DNA;

ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BASE PAIRING; BAYES THEOREM; CHEMISTRY; DNA SEQUENCE; ELECTROPHORESIS; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROBABILITY;

ARTIFICIAL INTELLIGENCE; BASE PAIRING; BASE SEQUENCE; BAYES THEOREM; DNA; ELECTROPHORESIS; MARKOV CHAINS; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA;

EID: 34547973378     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.1027     Document Type: Article

References (17)

1. C. Andrieu, J. Freitas, and A. Doucet, "Robust Full Bayesian Learning for Neural Networks," Neural Computing, vol. 13, pp. 2359-2407, 2001.
2. Applied Biosystems. "Applied Biosystems 3730/3730x1 DNA Analyzers: Sequencing Chemistry Guide: Rev B," http:// www.appliedbiosystems.com/, 2002.
3. P. Boufounos, S. El-Difrawy, and D. Ehrlich, "Basecalling Using Hidden Markov Models," J. Franklin Inst, vol. 341, pp. 23-36, 2004.
4. G. Casella and E.I. George, "Explaining the Gibbs Sampler," The Am. Statistician, vol. 46, pp. 167-174, Aug. 1992.
5. M. Chien et al., "The Genomic Sequence of the Accidental Pathogen Legionella Pneumophila," Science, vol. 305, pp. 1966-1968, 2004.
6. R. Durbin, S.R. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge Univ. Press, 1999.
7. B. Alberts et al., Essential Cell Biology. Garland Science, 2003.
8. B. Ewing, L. Hillier, M.C. Wendl, and P. Green, "Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assement," Genome Research, vol. 8, pp. 175-185, 1998.
9. W.R. Gilks, S. Richardson, and DJ. Spiegelhalter, Markov Chain Monte Carlo in Practice. Chapman & Hall, 1996.
10. N. Haan and S.J. Godsill, "Modelling Electropherogram Data for DNA Sequencing Using Variable Dimension," Proc. IEEE Int'l Conf. Acoustics, Speech, and Signal Processing (ICASSP '00), vol. 6, pp. 3542-3545, June 2000.
11. N. Haan and S.J. Godsill, "Sequential Methods for DNA Sequencing," Proc. IEEE Int'l Conf. Acoustics, Speech, and Signal Processing (ICASSP '01), vol. 2, pp. 1045-1048, May 2001.
12. Technelysium Pty Ltd., "Chromas," http://www.technelysium. com.au/chromas.html, 2004.
13. R.E. Mahony, G.D. Brushe, and J.B. Moore, "Hybrid Algorithms for Maximum Likelihood and Maximum A Posteriori Sequence Estimation," Proc. Int'l Conf. Signal Processing and Applications (ISSPA '96), 1996.
14. L.R. Rabiner, "A Tutorial on Hidden Markov Models and Selected Application in Speech Recognition," Proc. IEEE, vol. 77, no. 2, pp. 257-285, Feb. 1989.
15. F. Sanger, S. Nicklen, and A.R. Coulson, "DNA Sequencing with Chain-Terminating Inhibitors," Proc. Nat'l Academy of Sciences USA, vol. 74, pp. 5463-5467, 1977.
16. T. Vercauteren, A. Lopez, and X. Wang, "Estimating the Number of Competing Terminals in an IEEE 802.11 Wireless Network," Proc. IEEE Int'l Conf. Acoustics, Speech, and Signal Processing (ICASSP '05), Mar. 2005.
17. X. Zhou, X. Wang, R. Pal, I. Ivanov, M. Bittner, and E.R. Dougherty, "A Bayesian Connectivity-Based Approach to Constructing Probabilistic Gene Regulatory Networks," Bioinformatics, vol. 20, no. 17, pp. 2918-2927, Nov. 2004.