Indexing highly repetitive collections

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

Volumn 7643 LNCS, Issue , 2012, Pages 274-279

  Navarro, Gonzalo ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

COMPRESSED SUFFIX ARRAY; COMPUTATIONAL BIOLOGY; SOFTWARE REPOSITORIES;

ALGORITHMS; BIOINFORMATICS;

COMBINATORIAL MATHEMATICS;

EID: 84871656313     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-35926-2_29     Document Type: Conference Paper

References (26)

1. Abeliuk, A., Navarro, G.: Compressed Suffix Trees for Repetitive Texts. In: Calderón-Benavides, L., González-Caro, C., Chávez, E., Ziviani, N. (eds.) SPIRE 2012. LNCS, vol. 7608, pp. 30-41. Springer, Heidelberg (2012)
2. Bille, P., Landau, G., Raman, R., Sadakane, K., Rao Satti, S., Weimann, O.: Random access to grammar-compressed strings. In: Proc. 22nd SODA, pp. 373-389 (2011)
3. Chan, T., Larsen, K., Patrascu, M.: Orthogonal range searching on the RAM, revisited. In: Proc. 27th SoCG, pp. 1-10 (2011)
4. Charikar, M., Lehman, E., Liu, D., Panigrahy, R., Prabhakaran, M., Rasala, A., Sahai, A., Shelat, A.: Approximating the smallest grammar: Kolmogorov complexity in natural models. In: Proc. 34th STOC, pp. 792-801 (2002)
5. Charikar, M., Lehman, E., Liu, D., Panigrahy, R., Prabhakaran, M., Sahai, A., Shelat, A.: The smallest grammar problem. IEEE Trans. Inf. Theo. 51(7), 2554-2576 (2005)
6. Claude, F., Fariña, A., Martínez-Prieto, M., Navarro, G.: Compressed q-gram indexing for highly repetitive biological sequences. In: Proc. 10th BIBE, pp. 86-91 (2010)
7. Claude, F., Fariña, A., Martínez-Prieto, M., Navarro, G.: Indexes for highly repetitive document collections. In: Proc. 20th CIKM, pp. 463-468 (2011)
8. Claude, F., Navarro, G.: Improved Grammar-Based Compressed Indexes. In: Calderón-Benavides, L., González-Caro, C., Chávez, E., Ziviani, N. (eds.) SPIRE 2012. LNCS, vol. 7608, pp. 180-192. Springer, Heidelberg (2012)
9. Do, H.-H., Jansson, J., Sadakane, K., Sung, W.-K.: Fast relative Lempel-Ziv self-index for similar sequences. In: Proc. FAW-AAIM, pp. 291-302 (2012)
10. Fischer, J., Mäkinen, V., Navarro, G.: Faster entropy-bounded compressed suffix trees. Theor. Comp. Sci. 410(51), 5354-5364 (2009)
11. 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)
12. Grossi, R., Gupta, A., Vitter, J.: High-order entropy-compressed text indexes. In: Proc. 14th SODA, pp. 841-850 (2003)
13. Grossi, R., Vitter, J.: Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comp. 35(2), 378-407 (2006)
14. 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)
15. Kärkkäinen, J.: Repetition-Based Text Indexing. PhD thesis, Dept of Comp. Sci., Univ. of Helsinki, Finland (1999)
16. Kreft, S., Navarro, G.: On compressing and indexing repetitive sequences. Theor. Comp. Sci. (to appear, 2012);
17. Earlier versions in Proc. DCC 2010 and Proc. CPM 2011
18. Mäkinen, V., Navarro, G., Sirén, J., Välimäki, N.: Storage and retrieval of highly repetitive sequence collections. J. Comp. Biol. 17(3), 281-308 (2010)
19. Manber, U., Myers, E.: Suffix arrays: a new method for on-line string searches. SIAM J. Comp., 935-948 (1993)
20. Manzini, G.: An analysis of the Burrows-Wheeler transform. J. ACM 48(3), 407-430 (2001)
21. Maruyama, S., Nakahara, M., Kishiue, N., Sakamoto, H.: ESP-Index: A Compressed Index Based on Edit-Sensitive Parsing. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds.) SPIRE 2011. LNCS, vol. 7024, pp. 398-409. Springer, Heidelberg (2011)
22. Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Comp. Surv. 39(1), article 2 (2007)
23. Rytter, W.: Application of Lempel-Ziv factorization to the approximation of grammar-based compression. Theo. Comp. Sci. 302(1-3), 211-222 (2003)
24. Sadakane, K.: New text indexing functionalities of the compressed suffix arrays. J. Alg. 48(2), 294-313 (2003)
25. Ziv, J., Lempel, A.: A universal algorithm for sequential data compression. IEEE Trans. Inf. Theo. 23(3), 337-343 (1977)
26. Ziv, J., Lempel, A.: Compression of individual sequences via variable-rate coding. IEEE Trans. Inf. Theo. 24(5), 530-536 (1978)