Fast relative Lempel-Ziv self-index for similar sequences

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

Volumn 7285 LNCS, Issue , 2012, Pages 291-302

  Do, Huy Hoang ^a   Jansson, Jesper ^b   Sadakane, Kunihiko ^c   Sung, Wing Kin ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b OCHANOMIZU UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPRESSION SCHEME; SELF-INDEX; SUB-STRINGS; WEB TECHNOLOGIES;

COMPRESSION RATIO (MACHINERY); DATA STRUCTURES;

ALGORITHMS;

EID: 84861205393     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-29700-7_27     Document Type: Conference Paper

References (26)

1. The 1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature 467(7319), 1061-1073 (2010)
2. Bille, P., Landau, G.M., Raman, R., Sadakane, K., Satti, S.R., Weimann, O.: Random access to grammar-compressed strings. In: SODA, pp. 373-389 (2011)
3. Cao, M.D., Dix, T.I., Allison, L., Mears, C.: A simple statistical algorithm for biological sequence compression. In: DCC, pp. 43-52 (2007)
4. Chan, T.M., Larsen, K.G., Pǎ;traşcu, M.: Orthogonal range searching on the RAM, revisited. In: SoCG, pp. 1-10 (2011)
5. Christley, S., Lu, Y., Li, C., Xie, X.: Human genomes as email attachments. Bioinformatics 25(2), 274-275 (2009)
6. Claude, F., Navarro, G.: Self-indexed Text Compression Using Straight-Line Programs. In: Královič, R., Niwiński, D. (eds.) MFCS 2009. LNCS, vol. 5734, pp. 235-246. Springer, Heidelberg (2009)
7. Ferragina, P., Manzini, G.: Compression boosting in optimal linear time using the Burrows-Wheeler Transform. In: SODA, pp. 655-663 (2004)
8. Ferragina, P., Manzini, G.: Indexing compressed text. Journal of the ACM 52(4), 552-581 (2005)
9. Fischer, J., Heun, V.: A New Succinct Representation of RMQ-Information and Improvements in the Enhanced Suffix Array. In: Chen, B., Paterson, M., Zhang, G. (eds.) ESCAPE 2007. LNCS, vol. 4614, pp. 459-470. Springer, Heidelberg (2007)
10. Gagie, T., Gawrychowski, P., Kärkkäinen, J., Nekrich, Y., Puglisi, S.J.: A Faster Grammar-Based Self-index. In: Dediu, A.-H., Martín-Vide, C. (eds.) LATA 2012. LNCS, vol. 7183, pp. 240-251. Springer, Heidelberg (2012)
11. Golynski, A., Munro, J.I., Rao, S.S.: Rank/select operations on large alphabets: a tool for text indexing. In: SODA, pp. 368-373 (2006)
12. Grumbach, S., Tahi, F.: Compression of DNA sequences. In: DCC, pp. 340-350 (1993)
13. Huang, S., Lam, T.W., Sung, W.K., Tam, S.L., Yiu, S.M.: Indexing Similar DNA Sequences. In: Chen, B. (ed.) AAIM 2010. LNCS, vol. 6124, pp. 180-190. Springer, Heidelberg (2010)
14. Kreft, S., Navarro, G.: LZ77-like compression with fast random access. In: DCC, pp. 239-248 (2010)
15. Kreft, S., Navarro, G.: Self-indexing Based on LZ77. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 41-54. Springer, Heidelberg (2011)
16. Kuruppu, S., Puglisi, S.J., Zobel, J.: Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval. In: Chavez, E., Lonardi, S. (eds.) SPIRE 2010. LNCS, vol. 6393, pp. 201-206. Springer, Heidelberg (2010)
17. Kuruppu, S., Puglisi, S.J., Zobel, J.: Reference Sequence Construction for Relative Compression of Genomes. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds.) SPIRE 2011. LNCS, vol. 7024, pp. 420-425. Springer, Heidelberg (2011)
18. Mäkinen, V., Navarro, G.: Implicit Compression Boosting with Applications to Self-indexing. In: Ziviani, N., Baeza-Yates, R. (eds.) SPIRE 2007. LNCS, vol. 4726, pp. 229-241. Springer, Heidelberg (2007)
19. Mäkinen, V., Navarro, G., Sirén, J., Välimäki, N.: Storage and retrieval of highly repetitive sequence collections. J. of Computational Biology 17(3), 281-308 (2010)
20. Muthukrishnan, S.: Efficient algorithms for document retrieval problems. In: SODA, pp. 657-666 (2002)
21. Nekrich, Y.: Orthogonal range searching in linear and almost-linear space. Computational Geometry 42(4), 342-351 (2009)
22. Pǎ;traşcu, M.: Succincter. In: FOCS, pp. 305-313 (2008)
23. Rytter, W.: Application of Lempel-Ziv factorization to the approximation of grammar-based compression. Theoretical Computer Science 302, 211-222 (2003)
24. Sirén, J., Välimäki, N., Mäkinen, V., Navarro, G.: Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. In: Amir, A., Turpin, A., Moffat, A. (eds.) SPIRE 2008. LNCS, vol. 5280, pp. 164-175. Springer, Heidelberg (2008)
25. Willard, D.E.: Log-logarithmic worst-case range queries are possible in space Θ(N). Information Processing Letters 17(2), 81-84 (1983)
26. Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Transactions on Information Theory 23(3), 337-343 (1977)