Distributed string mining for high-throughput sequencing data

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

Volumn 7534 LNBI, Issue , 2012, Pages 441-452

  Välimäki, Niko ^a,b   Puglisi, Simon J ^b  

^a HELSINKI INSTITUTE FOR INFORMATION TECHNOLOGY   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

AMAZON EC2; DATA SETS; HIGH-THROUGHPUT; MAIN MEMORY; METAGENOMICS; OPTIMAL TIME; STATE-OF-THE-ART METHODS; SUB-STRINGS; TIME-SPACE TRADEOFFS;

BIOINFORMATICS; COMMERCE;

ALGORITHMS;

EID: 84866702034     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_35     Document Type: Conference Paper

References (16)

1. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. J. Discrete Algorithms 2(1), 53-86 (2004)
2. Birzele, F., Kramer, S.: A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics 22(24), 2628-2634 (2006)
3. Chan, S., Kao, B., Yip, C.L., Tang, M.: Mining emerging substrings. In: Proc. DASFAA, pp. 119-126. IEEE (2003)
4. Devroye, L., Szpankowski, W., Rais, B.: A note on the height of suffix trees. SIAM J. Comput. 21(1), 48-53 (1992)
5. Dhaliwal, J., Puglisi, S.J., Turpin, A.: Practical efficient string mining. IEEE Transactions on Knowledge and Data Engineering 24(4), 735-744 (2012)
6. Fischer, J., Heun, V., Kramer, S.: Optimal String Mining Under Frequency Constraints. In: Fürnkranz, J., Scheffer, T., Spiliopoulou, M. (eds.) PKDD 2006. LNCS (LNAI), vol. 4213, pp. 139-150. Springer, Heidelberg (2006)
7. Fischer, J., Mäkinen, V., Välimäki, N.: Space-efficient string mining under frequency constraints. In: Proc. ICDM, pp. 193-202. IEEE (2008)
8. Hui, L.C.K.: Color Set Size Problem with Application to String Matching. In: Apostolico, A., Galil, Z., Manber, U., Crochemore, M. (eds.) CPM 1992. LNCS, vol. 644, pp. 230-243. Springer, Heidelberg (1992)
9. Amazon Inc. Amazon elastic compute cloud (Amazon EC2), http://aws.amazon.com/ec2/#pricing (accessed May 2012)
10. Jacquet, P., Szpankowski, W.: Autocorrelation on words and its applications - analysis of suffix trees. Journal of Combinatorial Theory A 66, 237-269 (1994)
11. Kärkkäinen, J., Manzini, G., Puglisi, S.J.: Permuted Longest-Common-Prefix Array. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009. LNCS, vol. 5577, pp. 181-192. Springer, Heidelberg (2009)
12. Kärkkäinen, J., Sanders, P., Burkhardt, S.: Linear work suffix array construction. Journal of the ACM 53, 918-936 (2006)
13. 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)
14. Kügel, A., Ohlebusch, E.: A space efficient solution to the frequent string mining problem for many databases. Data Mining and Knowl. Discovery 17, 24-38 (2008)
15. Manber, U., Myers, E.W.: Suffix arrays: a new method for on-line string searches. SIAM Journal on Computing 22(5), 935-948 (1993)
16. Qin, J., et al.: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285), 59-65 (2010)