Space-efficient computation of maximal and supermaximal repeats in genome sequences

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

Volumn 7608 LNCS, Issue , 2012, Pages 99-110

  Beller, Timo ^a   Berger, Katharina ^a   Ohlebusch, Enno ^a  

^a UNIVERSITY OF ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATION THEORY; GENES; GENETIC ENGINEERING; INFORMATION RETRIEVAL; TREES (MATHEMATICS);

BURROWS WHEELER TRANSFORM; COMPUTATIONAL BIOLOGY; GENOME SEQUENCES; MAXIMAL REPEATS; SPACE EFFICIENT; SPACE EFFICIENT ALGORITHMS; THEORY AND PRACTICE; WAVELET TREE;

COMPUTATIONAL EFFICIENCY;

EID: 84867516521     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-34109-0_11     Document Type: Conference Paper

References (19)

1. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms 2, 53-86 (2004)
2. Becher, V., Deymonnaz, A., Heiber, P.: Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome. Bioinformatics 25(14), 1746-1753 (2009)
3. Beller, T., Gog, S., Ohlebusch, E., Schnattinger, T.: Computing the Longest Common Prefix Array Based on the Burrows-Wheeler Transform. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds.) SPIRE 2011. LNCS, vol. 7024, pp. 197-208. Springer, Heidelberg (2011)
4. Burrows, M., Wheeler, D.J.: A block-sorting lossless data compression algorithm. Research Report 124, Digital Systems Research Center (1994)
5. Culpepper, J.S., Navarro, G., Puglisi, S.J., Turpin, A.: Top-k Ranked Document Search in General Text Databases. In: de Berg, M., Meyer, U. (eds.) ESA 2010, Part II. LNCS, vol. 6347, pp. 194-205. Springer, Heidelberg (2010)
6. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proc. IEEE Symposium on Foundations of Computer Science, pp. 390-398 (2000)
7. Franek, F., Smyth, W.F., Tang, Y.: Computing all repeats using suffix arrays. Journal of Automata, Languages and Combinatorics 8(4), 579-591 (2003)
8. Gog, S., Ohlebusch, E.: Lightweight LCP-array construction in linear time (2011), http://arxiv.org/pdf/1012.4263
9. Grossi, R., Gupta, A., Vitter, J.S.: High-order entropy-compressed text indexes. In: Proc. 14th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 841-850 (2003)
10. Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, New York (1997)
11. Haas, B.J., Salzberg, S.L.: Finding repeats in genome sequences. In: Lengauer, T. (ed.) Bioinformatics - From Genomes to Therapies, Volume 1: Molecular Sequences and Structures, ch. 7, Wiley-VCH Verlag (2007)
12. Kasai, T., Lee, G., Arimura, H., Arikawa, S., Park, K.: Linear-Time Longest- Common-Prefix Computation in Suffix Arrays and Its Applications. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 181-192. Springer, Heidelberg (2001)
13. Kulekci, M.O., Vitter, J.S., Xu, B.: Efficient maximal repeat finding using the Burrows-Wheeler transform and wavelet tree. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(2), 421-429 (2012)
14. Narisawa, K., Inenaga, S., Bannai, H., Takeda, M.: Efficient Computation of Substring Equivalence Classes with Suffix Arrays. In: Ma, B., Zhang, K. (eds.) CPM 2007. LNCS, vol. 4580, pp. 340-351. Springer, Heidelberg (2007)
15. Okanohara, D., Sadakane, K.: A Linear-Time Burrows-Wheeler Transform Using Induced Sorting. In: Karlgren, J., Tarhio, J., Hyyr, H. (eds.) SPIRE 2009. LNCS, vol. 5721, pp. 90-101. Springer, Heidelberg (2009)
16. Prieur, E., Lecroq, T.: On-line construction of compact suffix vectors and maximal repeats. Theoretical Computer Science 407(1-3), 290-301 (2008)
17. Puglisi, S.J., Smyth, W.F., Turpin, A.: A taxonomy of suffix array construction algorithms. ACM Computing Surveys 39(2), 1-31 (2007)
18. Puglisi, S.J., Smyth, W.F., Yusufu, M.: Fast, practical algorithms for computing all the repeats in a string. Mathematics in Computer Science 3(4), 373-389 (2010)
19. Raffinot, M.: On maximal repeats in strings. Information Processing Letters 80(3), 165-169 (2001)