Characterization and extraction of irredundant tandem motifs

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

Volumn 7608 LNCS, Issue , 2012, Pages 385-397

  Parida, Laxmi ^a   Pizzi, Cinzia ^b   Rombo, Simona E ^c  

^a IBM T J WATSON RESEARCH CENTER   (United States)

^b UNIVERSITY OF PADOVA   (Italy)

^c UNIVERSITY OF CALABRIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

INFORMATION RETRIEVAL; REDUNDANCY;

CANDIDATE SETS; INPUT STRING; MAXIMALITY; MAXIMUM DISTANCE; SUBWORDS; TEXT STRING;

EXTRACTION;

EID: 84867529980     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-34109-0_41     Document Type: Conference Paper

References (21)

1. Apostolico, A., Comin, M., Parida, L.: VARUN: Discovering extensible motifs under saturation constraints. IEEE/ACM Trans. Comp. Biol. Bioinf. 7(4), 752-762 (2010)
2. Apostolico, A., Parida, L.: Incremental paradigms of motif discovery. J. of Comp. Biol. 11(1), 15-25 (2004)
3. Apostolico, A., Pizzi, C., Satta, G.: Optimal Discovery of Subword Associations in Strings. In: Suzuki, E., Arikawa, S. (eds.) DS 2004. LNCS (LNAI), vol. 3245, pp. 270-277. Springer, Heidelberg (2004)
4. Apostolico, A., Pizzi, C., Ukkonen, E.: Efficient algorithms for the discovery of gapped factors. Algorithms for Molecular Biology (6:5) (2011)
5. Apostolico, A., Satta, G.: Discovering subword associations in strings in time linear in the output size. J. Discrete Algorithms 7(2), 227-238 (2009)
6. Apostolico, A., Tagliacollo, C.: Incremental discovery of the irredundant motif bases for all suffixes of a string in o(n2logn) time. Theor. Comput. Sci. 408(2-3), 106-115 (2008)
7. Apostolico, A., Tagliacollo, C.: Optimal extraction of irredundant motif bases. Int. J. Found. Comput. Sci. 21(6), 1035-1047 (2010)
8. 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 Trans. Comput. Biology Bioinform. 3(2), 126-140 (2006)
9. Fassetti, F., Greco, G., Terracina, G.: Mining loosely structured motifs from biological data. IEEE Trans. Knowl. Data Eng. 20(11), 1472-1489 (2008)
10. Grossi, R., Pietracaprina, A., Pisanti, N., Pucci, G., Upfal, E., Vandin, F.: MADMX: A strategy for maximal dense motif extraction. J. of Comp. Biol. 18(4), 535-545 (2011)
11. Grossi, R., Pisanti, N., Crochemore, M., Sagot, M.-F.: Bases of motifs for generating repeated patterns with wild cards. IEEE/ACM Trans. Comp. Biol. Bioinf. 2(3), 159-177 (2005)
12. Marsan, L., Sagot, M.-F.: Algorithms for extracting structured motifs using a suffix tree with an applica ion to promoter and regulatory site consensus identification. J. of Comp. Biol. 7(3-4) (2000)
13. Marsan, L., Sagot, M.-F.: Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification. In: Proceedings of the fourth annual international conference on Computational Molecular Biology (RECOMB), pp. 210-219 (2000)
14. Monteiro, P.T., Mendes, N.D., Teixeira, M.C., others: Yeastract-discoverer: new tools to improve the analysis of transcriptional regulatory associations in saccharomyces cerevisiae. Nucleic Acids Research 36(Database-Issue), 132-136 (2008)
15. Mularoni, L., Guigó, R., Alba, M.M.: Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biol. 7(4), R33 (2006)
16. Parida, L., Rigoutsos, I., Floratos, A., Platt, D.E., Gao, Y.: Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm. In: Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 297-308 (2000)
17. PelfrËene, J., Abdeddam, S., Alexandre, J.: Extracting approximate patterns. J. Discrete Algorithms 3(2-4), 293-320 (2005)
18. Pisanti, N., Crochemore, M., Grossi, R., Sagot, M.-F.: A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum. In: Rovan, B., Vojtá?s, P. (eds.) MFCS 2003. LNCS, vol. 2747, pp. 622-631. Springer, Heidelberg (2003)
19. Pisanti, N., Crochemore, M., Grossi, R., Sagot, M.-F.: A comparative study of bases for motif inference. In: Iliopoulos, C., Lecroq, T. (eds.) String Algorithmics, pp. 195-226. KCL Publications (2004)
20. Rombo, S.E.: Extracting string motif bases for quorum higher than two. Theor. Comput. Sci (2012)
21. Ukkonen, E.: Maximal and minimal representations of gapped and non-gapped motifs of a string. Theor. Comput. Sci. 410(43), 4341-4349 (2009)