A more efficient closest string algorithm

2nd International Conference on Bioinformatics and Computational Biology 2010, BICoB 2010

Volumn , Issue , 2010, Pages 210-215

  Zhao, Ruixuan ^a   Zhang, Ning ^b  

^a SUN YAT SEN UNIVERSITY   (China)

^b UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Fixed parameter algorithms; The closest string

Indexed keywords

BEST-KNOWN ALGORITHMS; CLOSEST STRING; CLOSEST STRING PROBLEM; DRUG DESIGN; FIXED-PARAMETER ALGORITHMS; GENETIC PROBE; MOTIF FINDING; TIME COMPLEXITY;

ALGORITHMS; BIOINFORMATICS; DESIGN; HAMMING DISTANCE; PARAMETER ESTIMATION;

COMPUTATIONAL COMPLEXITY;

EID: 84883591872     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (21)

1. Lucas, K., Busch, M., MÖssinger, S., Thompson, J.A.: An improved microcomputer program for finding geneor gene family-specific oligonucleotides suitable as primers for polymerase chain reactions or as probes. CABIOS 7, 525-529 (1991)
2. Lanctot, K., Li, M., Ma, B., Wang, S., Zhang, L.: Distinguishing string selection problems. In: Proc. 10th ACM-SIAM Symp. on Discrete Algorithms, pp. 633-642 (1999)
3. Dopazo, J., Rodríguez, A., śaiz, J.C., Sobrino, F.: Design of primers for PCR amplification of highly variable genomes. CABIOS 9, 123-125 (1993)
4. Proutski, V., Holme, E.C.: Primer master: A new program for the design and analysis of PCR primers. CABIOS 12, 253-255 (1996)
5. Gramm, J., Huffner, F., Niedermeier, R.: Closest strings, primer design, and motif search. In: Currents in Computational Molecular Biology, poster abstracts of RECOMB 2002, pp. 74-75 (2002)
6. Wang, Y., Chen, W., Li, X., Cheng, B.: Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA. BMC Bioinformatics 7(suppl. 4), S9 (2006)
7. Deng, X., Li, G., Li, Z., Ma, B., Wang, L.: Genetic design of drugs without sideeffects. SIAM Journal on Computing 32(4), 1073-1090 (2003)
8. Ben-Dor, A., Lancia, G., Perone, J., Ravi, R.: Banishing bias from consensus sequences. In: Hein, J., Apostolico, A. (eds.) CPM 1997. LNCS, Vol. 1264, pp. 247-261. Springer, Heidelberg (1997)
9. Wang, L., Dong, L.: Randomized algorithms for motif detection. Journal of Bioinformatics and Computational Biology 3(5), 1039-1052 (2005)
10. Davila, J., Balla, S., Rajasekaran, S.: Space and time efficient algorithms for planted motif search. In: Proceedings of International Conference on Computational Science, vol. (2), pp. 822-829 (2006)
11. Fellows, M.R., Gramm, J., Niedermeier, R.: On the parameterized intractability of motif search problems. Combinatorica 26(2), 141-167 (2006)
12. Frances, M., Litman, A.: On covering problems of codes. Theoretical Computer Science 30, 113-119 (1997)
13. Li, M., Ma, B., Wang, L.: On the closest string and substring problems. J. ACM 49(2), 157-171 (2002)
14. Ma, B., Sun, X.: More Efficient Algorithms for Closest String and Substring Problems. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), Vol. 4955, pp. 396-409. Springer, Heidelberg (2008)
15. Marx, D.: Closest Substring Problems with Small Distance. SIAM. J. Comput., Vol 38(4), 1382-1410 (2008)
16. Gramm, J., Guo, J., Niedermeier, R.: On exact and approximation algorithms for distinguishing substring selection. In: Lingas, A., Nilsson, B.J. (eds.) FCT 2003. LNCS, Vol. 2751, pp. 195-209. Springer, Heidelberg (2003)
17. Gramm, J., Niedermeier, R., Rossmanith, P.: Fixed-Parameter Algorithms for CLOSEST STRING and Related Problems. Algorithmica 37(1), 25-42 (2003)
18. Stojanovic, N., Berman, P., Gumucio, D., Hardison, R., Miller, W.: A linear-time algorithm for the 1-mismatch problem. In: Proceedings of the 5th International Workshop on Algorithms and Data Structures, pp. 126-135 (1997)
19. Li, M., Ma, B., Wang, L.: Finding Similar Regions in Many Strings. In: Proceedings of the Thirty-first Annual ACM Symposium on Theory of Computing, Atlanta, pp.473-482 (1999)
20. Li, M., Ma, B., Wang, L.: Finding Similar Regions in Many Sequences. J. Comput. Syst. Sci. 65(1-2), 111-132 (2002); special issue for Thirty-first Annual ACM Symposium on Theory of Computing (1999)
21. Wang, L., Zhu, B.: Efficient Algorithms for the Closest String and Distinguishing String Selection Problems. FAW 2009: 261-270