On the complexity of finding gapped motifs

Journal of Discrete Algorithms

Volumn 8, Issue 2, 2010, Pages 131-142

  Michael, Morris ^a   Nicolas, François ^a   Ukkonen, Esko ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Gapped pattern; Motif discovery; NP complete; String matching with don't care symbols; Tandem motifs

Indexed keywords

ALPHABET SYMBOLS; DECISION PROBLEMS; INPUT STRING; MOTIF DISCOVERY; NP COMPLETE; OPTIMIZATION PROBLEMS; STRING MATCHING; TIME ALGORITHMS;

ALGOL (PROGRAMMING LANGUAGE);

POLYNOMIALS;

EID: 77649236716     PISSN: 15708667     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jda.2009.12.001     Document Type: Article

References (19)

1. Apostolico A., and Parida L. Incremental paradigms of motif discovery. J. of Computational Biology 11 1 (2004) 15-25
2. Arimura H., and Uno T. An efficient polynomial space and polynomial delay algorithm for enumeration of maximal motifs in a sequence. J. of Combinatorial Optimization 13 3 (2007) 243-262
3. Babcock W.C. Intermodulation interference in radio systems. Bell System Technical Journal 32 1 (1953) 63-73
4. Crochemore M., Iliopoulos C.S., Mohamed M., and Sagot M.-F. Longest repeats with a block of k don't cares. Theoretical Computer Science 362 1-3 (2006) 248-254
5. Das G., Fleischer R., Ga̧sieniec L., Gunopulos D., and Kärkkäinen J. Episode matching. In: Apostolico A., and Hein J. (Eds). Proc. of the 8th Annual Symposium on Combinatorial Pattern Matching. CPM'1997. LNCS vol. 1264 (1997), Springer-Verlag 12-27
6. Gusfield D. Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology (1997), Cambridge University Press
7. Karp R.M. Reducibility among combinatorial problems. In: Miller R.E., and Thatcher J.W. (Eds). Complexity of Computer Computations (1972), Plenum Press 85-103
8. Kolpakov R.M., and Kucherov G. Finding maximal repetitions in a word in linear time. Proc. of the 40th Annual Symposium on Foundations of Computer Science. FOCS'1999 (1999), IEEE Computer Society 596-604
9. Kolpakov R.M., and Kucherov G. Finding approximate repetitions under Hamming distance. Theoretical Computer Science 303 1 (2003) 135-156
10. Kevin Lanctot J., Li M., Ma B., Wang S., and Zhang L. Distinguishing string selection problems. Information and Computation 185 1 (2003) 41-55
11. Landau G.M., Schmidt J.P., and Sokol D. An algorithm for approximate tandem repeats. J. of Computational Biology 8 1 (2001) 1-18
12. Li M., Ma B., and Wang L. Finding similar regions in many sequences. J. of Computer and System Sciences 65 1 (2002) 73-96
13. Marsan L., and Sagot M.-F. Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. of Computational Biology 7 3-4 (2000) 345-362
14. Nicolas F., and Rivals E. Hardness of optimal spaced seed design. J. of Computer and System Sciences 74 5 (2008) 831-849
15. L. Parida, I. Rigoutsos, A. Floratos, D.E. Platt, Y. Gao, Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm, in: Proc. of the 11th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA'2000, 2000, pp. 297-308
16. Pelfrêne J., Abdeddaïm S., and Alexandre J. Extracting approximate patterns. J. of Discrete Algorithms 3 2-4 (2005) 293-320
17. Pisanti N., Crochemore M., Grossi R., and Sagot M.-F. Bases of motifs for generating repeated patterns with wild cards. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 1 (2005) 40-49
18. Rocke E. Using suffix trees for gapped motif discovery. In: Giancarlo R., and Sankoff D. (Eds). Proc. of the 11th Annual Symposium on Combinatorial Pattern Matching. CPM'2000. LNCS vol. 1848 (2000), Springer-Verlag 335-349
19. Storer J.A. Data Compression: Methods and Theory. Principles of Computer Science vol. 13 (1988), Computer Science Press