A simple and fast DNA compressor

Software - Practice and Experience

Volumn 34, Issue 14, 2004, Pages 1397-1411

  Manzini, Giovanni ^a   Rastero, Marcella ^a  

^a UNIVERSITY OF EASTERN PIEDMONT   (Italy)

Author keywords

Approximate repeats encoding; Data compression; DNA sequences; Space economical algorithms

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; DATABASE SYSTEMS; DNA SEQUENCES; PROBLEM SOLVING; RANDOM PROCESSES;

APPROXIMATE REPEATS ENCODING; MUTATIONS; SPACE ECONOMICAL ALGORITHMS; SUBSTRINGS;

DATA COMPRESSION;

EID: 8344261403     PISSN: 00380644     EISSN: None     Source Type: Journal    
DOI: 10.1002/spe.619     Document Type: Article

References (20)

1. Lanctot JK, Li M, Yang E. Estimating DNA sequence entropy. Proceedings of the 11th ACM-SIAM Symposium on Discrete Algorithms (SODA '00). SIAM Press, 2000; 409-418.
2. Chen X, Kwong S, Li M. A compression algorithm for DNA sequences and its applications in genome comparison. Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00). ACM Press: New York, 2000.
3. Li M, Badger JH, Chen X, Kwong S, Kearney P, Zhang H. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001; 17(2):149-154.
4. Allison L, Stern L, Edgoose T, Dix TI. Sequence complexity for biological sequence analysis. Computers and Chemistry 2000; 24(1):43-55.
5. Bennet C, Li M, Ma B. Chain letters and evolutionary histories. Scientific American 2003; 32-37.
6. Milosavjevic A. Discovering by minimal length encoding: A case study in molecular evolution. Machine Learning 1993; 12:68-87.
7. Witten IH, Neal RN, Cleary JG. Arithmetic coding for data compression. Communications of the ACM 1987; 30(6):520-540.
8. Grumbach S, Tahi F. A new challenge for compression algorithms: Genetic sequences. Information Processing and Management 1994; 30(6):875-886.
9. Apostolico A, Lonardi S. Compression of biological sequences by greedy off-line textual substitution. Proceedings Data Compression Conference, Snowbird, UT, 2000, Storer JA, Cohn M (eds.). IEEE Computer Society Press: Los Alamitos, CA, 2000; 143-152.
10. Matsumoto T, Sadakane K, Imai H. Biological sequence compression algorithms. Proceedings of the Genome Informatics Workshop. Universal Academy Press: Tokyo, 2000; 43-52.
11. Chen X, Li M, Ma B, Tromp J. DNACompress: Fast and effective DNA sequence compression. Bioinformatics 2002; 18(12):1696-1698.
12. Ma B, Tromp J, Li M. PatternHunter - fast and more sensitive homology search. Bioinformatics 2002; 18:440-445.
13. Apostolico A, Lonardi S. Off-line compression by greedy textual substitution. Proceedings of the IEEE 2000; 88(11):1733-1744.
14. Karp R, Rabin M. An efficient randomized pattern-matching algorithms. IBM Journal of Research and Development 1987; 31(2):249-260.
15. Bentley J, McIlroy D. Data compression with long repeated strings. Information Sciences 2001; 135:1-11.
16. Williams H, Zobel J. Compressing integers for fast file access. The Computer Journal 1999; 42(3):193-201.
17. National Center for Biotechnology Information, http://www.ncbi.nih.gov [2003].
18. Witten IH, Moffat A, Bell TC. Managing Gigabytes: Compressing and Indexing Documents and Images (2nd edn). Morgan Kaufmann: Los Altos, CA, 1999.
19. Lonardi S. Off-line home page, http://www.cs.ucr.edu/~stelo/Offline [2003].
20. Chen X. Personal communication, 2003.