Compressing biological sequences using self adjusting data structures

Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB

Volumn , Issue , 2010, Pages

  Antoniou, Dimitris ^a   Theodoridis, Evangelos ^a   Tsakalidis, Athanasios ^a  

^a UNIVERSITY OF PATRAS   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCES; SELF-ADJUSTING DATA STRUCTURES; SPLAY TREES;

DATA STRUCTURES; INFORMATION TECHNOLOGY;

DATA COMPRESSION;

EID: 79951623985     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ITAB.2010.5687689     Document Type: Conference Paper

References (12)

1. D.D. Steator and R.E. Tarjan, "Self-adjusting binary search trees," Journal of the ACM, 32:652-686, 1985.
2. E. D. Demaine, D. Harmon, J. Iacono, and M. Pǎtraşcu, "Dynamic optimality--almost," SIAM Journal on Computing, volume 37, number 1, pp. 240-251, 2007.
3. G. F. Georgakopoulos, "How to splay for log log n - competitiveness, " in WEA 2005, pp. 570-579.
4. C. C. Wang, J. Derryberry and D.D. Sleator, "O(log log n)-competitive dynamic binary search trees, " in ACM SODA 2006, pp. 374-383.
5. D. W. Jones, "Application of splay trees to data compression," in Communications of the ACM, August 1988, pp. 996-1007.
6. A. Apostolico and S. Lonardi, "Compression of biological sequences by greedy off-line textual substitution," in Proceedings Data Compression Conference, 2000, pp. 143-152. (Pubitemid 30588742)
7. S. Grumbach and F. Tahi. "A new challenge for compression algorithms: Genetic Sequences," in Inf Proc. and Management, 1994, 30(6):875-886. (Pubitemid 124012808)
8. X. Chen, S. Kwong, and M. Li. "A compression algorithm for DNA sequences and its applications in genome comparison," in Proceedings of the 4th Annual International Conference on Computational Molecular Biology (RECOMB-00). ACM Press, 2000.
9. X. Chen, M. Li, B. Ma, and J. Tromp. "DNACompress: fast and effective DNA sequence compression," Bioinformatics, 18(12): 1696-1698,2002. (Pubitemid 36097740)
10. M. Fürer, "Randomized splay trees," in Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms, January 17-19,1999, Baltimore, Maryland, United States, pp.903-904.
11. D.A. Huffman, "A method for the construction of minimumredundancy codes," in Proceedings of the I.R.E., September 1952, pp 1098-1102.
12. T. I. Dix, D. R. Powell, L. Allison, J. Bernal, S. Jaeger, L. Stem. "Comparative analysis of long DNA sequences by per element information content using different contexts," BMC Bioinformatics, 8(Suppl.2):S10,2007.