Genome compression using normalized maximum likelihood models for constrained Markov sources

2008 IEEE Information Theory Workshop, ITW

Volumn , Issue , 2008, Pages 261-265

  Tabus, Ioan ^a   Korodi, Gergely ^a  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

BLOCK CODES; CYBERNETICS; ENCODING (SYMBOLS); INFORMATION THEORY; MAXIMUM LIKELIHOOD; PROGRAMMING THEORY; STANDARDS;

CODING SCHEMES; CONSTRAINED MARKOV; FIRST ORDERS; HUMAN GENOMES; MARKOV SOURCES; MEMORYLESS SOURCES; NORMALIZED MAXIMUM LIKELIHOOD; NORMALIZED MAXIMUM LIKELIHOOD MODEL; SIMILARITY SCORES; STATE OF THE ARTS; UNIVERSAL CODING;

MARKOV PROCESSES;

EID: 51849091493     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ITW.2008.4578662     Document Type: Conference Paper

References (16)

1. M.S. Bartlett, "The frequency goodness of fit test for probability chains", Proceedings Cambridge Philosophical Society, vol. 47, pp. 86-95, 1950.
2. X. Chen, S. Kwong, and M. Li, "A Compression Algorithm for DNA Sequences", IEEE Engineering in Medicine and Biology, pp. 61-66, July/August 2001.
3. T. Cover, Enumerative source encoding, IEEE Transactions on Information Theory, Vol. 19, pp. 73-77, 1973.
4. L. Davisson, "Minimax noiseless universal coding for Markov sources", IEEE Transactions on Information Theory, vol. 29, no. 2, pp. 211-215, 1983.
5. S. Grumbach and F. Tahi, "A new challenge for compression algorithms: Genetic sequences", J. Inform. Process. Manage., vol. 30, no. 6, pp. 875-886, 1994.
6. P. Jacquet and W. Szpankowski, "Markov types and minimax redundancy for Markov sources", IEEE Transactions on Information Theory, vol. 50, no. 7, pp. 1393-1402, 2004.
7. G. Korodi and I. Tabus, "An efficient normalized maximum likelihood algorithm for DNA sequence compression", ACM Transactions on Information Systems, vol. 23, no. 1, pp. 3-34, 2005.
8. G. Korodi, I. Tabus, "Normalized maximum likelihood model of order-1 for the compression of DNA sequences", in Proc. IEEE Data Compression Conference, DCC'07, pp:33-42, Snowbird, 27-29 March 2007.
9. B. Ma, J. Tromp, and M. Li, "PatternHunter: Faster and More Sensitive Homology Search", Bioinformatics, vol. 18, pp. 440-445, 2002.
10. T. Matsumoto, K. Sadakane, and H. Imai, "Biological Sequence Compression Algorithms", Genome Informatics Workshop, Universal Academy Press, pp. 43-52, 2000.
11. J.J. Rissanen and G.G. Langdon, "Arithmetic Coding", IBM J. Research and Development, vol. 23, no. 2, pp. 149-162, March 1979.
12. J. Rissanen, "Fisher information and stochastic complexity", IEEE Transactions on Information Theory, vol. 42, pp. 40-47, Jan. 1996.
13. Y.M. Shtarkov. Universal sequential coding of single messages. Translated from Problems of Information Transmission, Vol. 23, No. 3, 3-17, July-September 1987.
14. I. Tabus, G. Korodi, and J. Rissanen, "DNA sequence compression using the normalized maximum likelihood model for discrete regression", Data Compression Conference 2003, DCC '03, pp. 253-262, 2003.
15. P. Whittle, "Some distribution and moment formulae for the Markov chain", Journal of the Royal Statistical Society. Series B (Methodological), vol. 17, no. 2, pp. 235-242, 1955.
16. The Human Genome, ftp://ftp.ncbi.nlm.nih.gov/genomes/H sapiens/April 14 2003