Efficient algorithms for the discovery of gapped factors

Algorithms for Molecular Biology

Volumn 6, Issue 1, 2011, Pages

  Apostolico, Alberto ^a,b   Pizzi, Cinzia ^a   Ukkonen, Esko ^c,d  

^a UNIVERSITY OF PADOVA   (Italy)

^b Georgia Institute of Technology   (United States)

^c UNIVERSITY OF HELSINKI   (Finland)

^d HELSINKI INSTITUTE FOR INFORMATION TECHNOLOGY   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79953086981     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-6-5     Document Type: Article

References (21)

1. Apostolico A, Bock ME, Lonardi S. Monotony of surprise and large-scale quest for unusual words. Journal of Computational Biology 2003, 10(3-4):238-311.
2. Apostolico A, Pizzi C. Motif discovery by monotone scores. Discrete Applied Mathematics, special issue Computational Molecular Biology Series 2007, 155(6-7):695-706.
3. Apostolico A, Pizzi C, Satta G. Optimal discovery of subword associations in strings (extended abstract). Proceedings of the Seventh International Conference on Discovery Science: 2-5 Oct 2004; Padova, Italy 2004, 270-277. Arikawa, Springer, LNAI 3245, Suzuki.
4. Peterlongo P, Allali J, Sagot MF. Indexing gapped factors using a tree. International Journal on Fundation of Computer Science 2008, 19:71-87.
5. Iliopoulos CS, Rahman MS. Indexing factors with gaps. Algorithmica 2007, 55:60-70.
6. Marsan L, Sagot MF. Extracting Structured Motifs Using a Suffix Tree - Algorithms and Application to Promoter Consensus Identification. Proceedings of the Fourth Annual International Conference on Computational Molecular Biology: 8-11 April 2000; Tokyo 2000, 210-219. ACM Press, Shamir, Miyano, Istrail, Pevzner, Waterman.
7. Eskin E, Pevzner P. Finding composite regulatory patterns in DNA Sequences. Bioinformatics 2002, 18:354-363.
8. Carvalho A, Freitas A, Oliveira A, Sagot M. Efficient extraction of structured motifs using box-links. Proceedings of the 11th Conference on String Processing and Information Retrieval: 5-8 Oct 2004; Padova, Italy 2004, 267-268. Springer LNCS 3246, Apostolico, Melucci.
9. Pisanti N, Carvahlo A, Marsan L, Sagot MF. RISOTTO: Fast extraction of motifs with mismatches. Proceedings of the LATIN 2006 - Theoretical Informatics, 7th Latin American Symposium: 20-24 March 2006; Valdivia, Chile 2006, 757-768. Springer LNCS 3887, Correa, Hevia, Kiwi.
10. van Helden J, Rios A, Collado-Vides J. Discovery regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acid Research 2000, 28(8):1808-1818.
11. Arimura H, Arikawa S. Efficient discovery of optimal word-association patterns in large text databases. New Generation Computing 2000, 28:49-60.
12. Wang JL, Chirn GW, Marr T, Shapiro B, Shasha D, Zhang K. Combinatorial pattern discovery for scientific data: some preliminary results. Proceedings of the 1994 ACM SIGMOD International Conference on Management of Data: 24-27 May 1994; Minneapolis, USA 1994, 115-125. ACM press, Snodgrass, Winslett.
13. Weiner P. Linear pattern matching algorithms. Proceedings of the 14th IEEE Annual Symposium on Switching and Automata Theory: 15-17 Oct 1973; Iowa, USA 1973, 1-11. IEEE Computer Society.
14. McCreight E. A space-economical suffix tree construction algorithm. Journal of the ACM 1976, 23(2):262-272.
15. Ukkonen E. On-line construction of suffix trees. Algorithmica 1995, 14(3):249-269.
16. Apostolico A. The myriad virtues of subword trees. Combinatorial Algorithms on Words, Volume F12 of NATO ASI Series 1985, 85-96. New York: Springer-Verlag, Apostolico, Galil.
17. Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology 1997, Cam-bridge: Cambridge University Press.
18. Apostolico A, Satta G. Discovering subword associations in strings in time linear in the output size. Journal of Discrete Algorithms 2009, 7(2):227-238.
19. Schieber B, Vishkin U. On finding lowest common ancestors: simplifications and parallelizations. SIAM Journal on Computing 1988, 17:1253-1262.
20. Inenaga S, Bannai H, Hyyrö H, Shinohara A, Takeda M, Nakai K, Miyano S. Finding optimal pairs of cooperative and competing Patterns with bounded distance. Proceedings of the Seventh International Conference on Discovery Science: 2-5 Oct 2004; Padova, Italy 2004, 32-46. Springer, LNAI 3245, Suzuki, Arikawa.
21. Tompa M, Li N, Bailey T, Church G, De Moor B, Es-kin E, Favorov A, Frith M, Fu Y, Kent W, Makeev V, AA M, Noble W, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 2005, 23:137-144. 10.1038/nbt1053, 15637633.