DNA sequence compression using the Burrows-Wheeler Transform

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002

Volumn , Issue , 2002, Pages 303-313

  Adjeroh, D ^a   Zhang, Y ^a   Mukherjee, A ^b   Powell, M ^c   Bell, T ^c  

^a West Virginia University   (United States)

^b University of Central Florida   (United States)

^c UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Burrows Wheeler Transform; BWT; DNA sequence compression; repetition structures

Indexed keywords

BACKWARD WAVE TUBES; BIOINFORMATICS; DATA COMPRESSION; DNA; PATTERN MATCHING; TREES (MATHEMATICS);

BIOLOGICAL SEQUENCES; BURROWS WHEELER TRANSFORM; OFF-LINE DICTIONARIES; OFF-LINE METHODS; REPEATING PATTERNS; SEQUENCE COMPRESSION; SUFFIX ARRAYS; SUFFIX-TREES;

DNA SEQUENCES;

DNA;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOLOGY; CHEMISTRY; CLASSIFICATION; DATA BASE; DNA SEQUENCE; GENETIC DATABASE; INFORMATION PROCESSING; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATA COMPRESSION; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DNA; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 13844291872     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CSB.2002.1039352     Document Type: Conference Paper

References (36)

1. Adjeroh D.A., Mukherjee A., Bell T.C., Powell M., and Zhang N., "Pattern matching in BWT-transformed text", Proceedings, IEEE Data Compression Conference, Snowbird, Utah, April 2-4, 2002.
2. Apostolico A. and Fraenkel A.S., "Robust transmission of unbounded strings using Fibonacci representations", IEEE Transactions on Information Theory, 33(2):238-245, 1987.
3. Apostolico A and Lonardi S, "Compression of biological sequences by greedy off-line textual substitution", Proceedings, IEEE Data Compression Conference, Snowbird, UT, 2001
4. Apostolico A and Lonardi S, "Offline compression by greedy textual substitution", Proceedings of the IEEE, 88 (11), 1733-1744, 2000
5. Bat O, Kimmel M., and Axelrod D. E, "Computer simulation of expansions of DNA triplet repeats in the Fragile X Syndrome and Huntington's disease", Journal of Theoretical Biology, 188, 53-67,. 1997
6. Bell T.C., Cleary J.C., and Witten I.H., Text Compression, Prentice Hall, Englewood Cliffs, NJ, 1990.
7. Bell T.C, Powell M., Mukherjee A. and Adjeroh D. A. "Searching BWT compressed text with the Boyer-Moore algorithm and binary search", Proceedings, IEEE Data Compression Conference, Snowbird, Utah, April 2-4, 2002. Available at: http://www.cosc.canterbury.ac.nz/tim/tmp/dcc02match.pdf.
8. Bentley J. L., Sleator D.D., Tarjan R.E., and Wei V., "A locally adaptive data compression scheme", Communications of the ACM, 29(4), 320-330, 1986.
9. Burrows M. and Wheeler D.J., "A block-sorting lossless data compression algorithm", Technical Report, Digital Equipment Corporation, Palo Alto, CA, 1994.
10. Chen X., Kwong S.and Li M, "A compression qlgorithm for DNA sequences and its applications in genome comparison", In Proceedings, 10th Workshop on Genome Informatics (GIW'99), pp. 52-61, 1999.
11. Cleary J.G. and Teahan W.J., "Unbounded length contexts for PPM", The Computer Journal, 40(2/3), 67-75, 1997
12. Collins F.S., Patrinos A., Jordan E, Chakravarti A, Gesteland, and Walters L, "New goals for the US Human Genome Project: 1998-2003", Sciecne 282(5389):682-689, 1998.
13. Elias. P., "Universal codeword sets and the representation of the integers", IEEE Transactions on Information Theory, 21:194-203, 1975.
14. Fenwick P., "The Burrows-Wheeler Transform for block sorting text compression", The Computer Journal, 39(9), 731-740, 1996.
15. Gatlin, L, Information Theory and the Living System, Columbia University Press, New York, 1972.
16. Giancarlo R., "A generalization of the suffix tree to square matrices, with applications", SIAM Journal on Computing, 24(3), 520-562, 1995.
17. Grumbach S and Tahi F., "A new challenge for compression algorithms: genetic sequences", Info. Processing & Management, 30: 875-886, 1994.
18. Gusfield D., Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, Cambridge, UK, 1997.
19. Herzel, H., Ebeling, W., and Schmitt, A, "Entropies of biosequences: The role of repeats", Physical Review E, 50(6):5061-5071, 1994.
20. Lanctot J. K., Li M. and Yang E., "Estimating DNA sequence entropy", Proceedings, 11th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA2000) , pp. 409-418, 2000.
21. Li M and Vit'anyi P, An Introduction to Kolmogorov Complexity and its Applications, Springer-Verlag, 1993.
22. Loewenstern, D. and Yainilos, P., "Significantly lower entropy estimates for natural DNA sequences", Proceedings, IEEE Data Compression Conference, Snowbird, UT, pp. 151-161, 1997.
23. Manber U. and Myers G., "Suffix arrays: A new method for on-line string searches", SIAM Journal of Computing, 22(5), 935-948, 1993.
24. Mantegna R.N, Buldyrev S.V., Goldberger A.L., Peng C.K., Simons M., and Stanley H.E., "Linguistic features of noncoding DNA sequences", Physical Review Letters, 73, 23, 3169-3172, 1994.
25. Matsumoto T., Sadakane K. and Imai H, "Biological sequence compression algorithms", Department of Information Science, University of Tokyo, 2000 . http://citeseer.nj.nec.com/457261.html
26. McCreight E. M., "A space-economical suffix tree construction algorithm", Journal of the ACM, 23(2), 262-272, 1976.
27. Nelson M., "Data Compression with the Burrows-Wheeler Transform", Dr. Dobb's Journal, Sept. 1996. http://dogma.net/markn/articles/bwt/bwt.htm
28. Nevill-Manning C.G and Witten I.H. "Online and off-line heuristics for infering hierarchies of repetitions in sequences", Proceedings of the IEEE, 88 (11), 1745-1755, 2000
29. Rivals E., Delahaye, J-P, Dauchet M. and Delgrange O., "A guaranteed compression scheme for repetitive DNA sequences", Proceedings, IEEE Data Compression Conference, Snowbird, UT, pp. 453
30. Rival, E., Delgrange, O., Delahaye, J.P., Dauchet, M., Delorme, M. Henaut, A. and Ollivier, E., "Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences", CABIOS, 13: 131-136, 1997
31. Rubin F., "Experiments in text file compression", Communications of the ACM, 19 (11), 617-623, 1976.
32. Storer, J.A. and Szymanski, T.G., "Data compression via textual substitution," Journal of the ACM ssociation for Computing Machinery, 29(4), 928-951, 1982.
33. Witten I. H., Moffat A. and Bell T. C., Managing Gigabytes: Compressing and Indexing Documents and Images, Morgan Kaufman, 1999.
34. Wolff, J. G., "Recoding of natural language for economy of transmission or storage," The Computer Journal. 21 (1), 42-44, 1978.
35. Ziv J. and Lempel A., "A universal algorithm for sequential data compression", IEEE Transactions on Information Theory, 23(3) 337-343, 1977.
36. Ziv J. and Lempel A., "Compression of individual sequences via variable rate coding", IEEE Transactions on Information Theory, 24(5), 530-536, 1978.