Component-based matching for multiple interacting RNA sequences

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

Volumn 6674 LNBI, Issue , 2011, Pages 73-86

  Badr, Ghada ^a,b   Turcotte, Marcel ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

^b University and Research District ^*  (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

BACKTRACKING SEARCH; CELLULAR PROCESS; COMPONENT BASED; DATABASE SIZE; EFFICIENT ALGORITHM; EXECUTION TIME; FAST ALGORITHMS; INPUT PATTERNS; INTERACTION PATTERN; LARGE DATABASE; POST-TRANSCRIPTIONAL GENE REGULATION; RNA INTERACTION; RNA SEQUENCES; WORST CASE;

ALGORITHMS; BIOINFORMATICS; DATA STRUCTURES; GENES;

RNA;

EID: 79955807323     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-21260-4_11     Document Type: Conference Paper

References (17)

1. Andronescu, M., Zhang, Z.C., Condon, A.: Secondary structure prediction of interacting RNA molecules. J. Mol. Biol. 345(5), 987-1001 (2005)
2. Anwar, M., Nguyen, T., Turcotte, M.: Identification of consensus RNA secondary structures using suffix arrays. BMC Bioinformatics 7, 244 (2006)
3. Badr, G.: Tries in information retrieval and syntactic pattern recognition. Ph.D. Thesis, School of Computer Science, Carleton University (June 2006)
4. Badr, G.: Optimized similarity measure over trie. In: MLDM Posters, pp. 236-150 (2007)
5. Bentley, J., Sedgewick, R.: Ternary search trees. Dr. Dobb's Journal (1998)
6. Carvalho, A.M., Freitas, A.T., Oliveira, A.L., Sagot, M.-F.: An efficient algorithm for the identification of structured motifs in DNA promoter sequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 3(2), 126-140 (2006)
7. Clement, J., Flajolet, P., Vallee, B.: The analysis of hybrid trie structures. In: Proc. Annual ACM-SIAM Symp. on Discrete Algorithms, San Francisco, California, pp. 531-539 (1998)
8. Gerlach, W., Giegerich, R.: GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics 22(6), 762-764 (2006)
9. Kato, Y., Akutsu, T., Seki, H.: A grammatical approach to RNA-RNA interaction prediction. Pattern Recognition 42(4), 531-538 (2009)
10. Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.: RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 26(18), i460-i466 (2010)
11. Marande, W., Burger, G.: Mitochondrial DNA as a genomic jigsaw puzzle. Science 318(5849), 415 (2007)
12. Marsan, L., Sagot, M.F.: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol. 7(3-4), 345-362 (2000)
13. O'Brien, E.A., Koski, L.B., Zhang, Y., Yang, L.S., Wang, E., Gray, M.W., Burger, G., Lang, B.F.: TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res. 35(Database issue), i445-i451 (2007)
14. Oommen, B.J., Badr, G.: Breadth-first search strategies for trie-based syntactic pattern recognition. Pattern Analysis and Applications 10(1), 1-13 (2007)
15. Pisanti, N., Carvalho, A.M., Marsan, L., Sagot, M.-F.: RISOTTO: Fast extraction of motifs with mismatches. In: Correa, J.R., Hevia, A., Kiwi, M. (eds.) LATIN 2006. LNCS, vol. 3887, pp. 757-768. Springer, Heidelberg (2006)
16. Salari, R., Backofen, R., Sahinalp, S.C.: Fast prediction of RNA-RNA interaction. Algorithms for Molecular Biology: AMB 5, 5 (2010)
17. Strothmann, D.: The affix array data structure and its applications to RNA secondary structure analysis. Theoretical Computer Science 389(1-2), 278-294 (2007)