Relative lempel-ziv compression of genomes for large-scale storage and retrieval

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6393 LNCS, Issue , 2010, Pages 201-206

  Kuruppu, Shanika ^a   Puglisi, Simon J ^b   Zobel, Justin ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b RMIT UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BASE SEQUENCES; FAST SEARCH; GENOMIC DATA; HUMAN GENOMES; POINT MUTATIONS; R-SEQUENCES; SELF-INDEX; STORAGE AND RETRIEVALS;

DATA STRUCTURES; INFORMATION RETRIEVAL; TOWERS; DIGITAL STORAGE;

GENES;

EID: 78449295543     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-16321-0_20     Document Type: Conference Paper

References (11)

1. Apostolico, A., Lonardi, S.: Compression of biological sequences by greedy off-line textual substitution. In: Proc. IEEE DCC, pp. 143-152 (2000)
2. Cao, M.D., Dix, T., Allison, L., Mears, C.: A simple statistical algorithm for biological sequence compression. In: Proc. IEEE DCC, pp. 43-52 (2007)
3. Chen, X., Kwong, S., Li, M.: A compression algorithm for DNA sequences and its applications in genome comparison. In: Proc. RECOMB, p. 107. ACM, New York (2000)
4. Christley, S., Lu, Y., Li, C., Xie, X.: Human genomes as email attachments. Bioinformatics 25(2), 274-275 (2009)
5. Grumbach, S., Tahi, F.: Compression of DNA sequences. In: Proc. IEEE DCC, pp. 340-350 (1993)
6. Kuruppu, S., Beresford-Smith, B., Conway, T., Zobel, J.: Repetition-based compression of large DNA datasets. In: Poster at RECOMB (2009)
7. Mäkinen, V., Navarro, G., Sirén, J., Välimäki, N.: Storage and retrieval of highly repetitive sequence collections. J. Computational Biology 17(3), 281-308 (2010)
8. Navarro, G., Mäkinen, V.: Compressed full text indexes. ACM Computing Surveys 39(1) (2007)
9. Okanohara, D., Sadakane, K.: Practical entropy-compressed rank/select dictionary. In: Proc. ALENEX. SIAM, Philadelphia (2007)
10. Rivals, E., Delahaye, J., Dauchet, M., Delgrange, O.: A guaranteed compression scheme for repetitive DNA sequences. In: Proc. IEEE DCC, p. 453 (1996)
11. Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Transactions on Information Theory 23(3), 337-343 (1977)