Dynamic neighborhood searches for thermodynamically designing DNA sequence

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

Volumn 4848 LNCS, Issue , 2008, Pages 130-139

  Kawashimo, Suguru ^a   Ono, Hirotaka ^a   Sadakane, Kunihiko ^a   Yamashita, Masafumi ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

DNA sequence design algorithm; Local search; Statistical thermodynamical constraints

Indexed keywords

CALCULATIONS; DNA; FLIGHT DYNAMICS; FREE ENERGY; GENES; GENETIC PROGRAMMING; HAMMING DISTANCE; LEARNING ALGORITHMS; NUCLEIC ACIDS; ORGANIC ACIDS;

COMPUTATIONAL EXPERIMENTS; DISTANCE BASED; DNA COMPUTING; DNA SEQUENCE DESIGN ALGORITHM; DYNAMIC NEIGHBORHOODS; EFFICIENT SEARCH; LOCAL SEARCH; MINIMUM FREE ENERGIES; NEIGHBORHOOD STRUCTURES; SEQUENCE DESIGN; SEQUENCE SETS; STATISTICAL THERMODYNAMICAL CONSTRAINTS;

SET THEORY;

EID: 49949096745     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-77962-9_13     Document Type: Conference Paper

References (23)

1. Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266(5187), 1021-1024 (1994)
2. Andronescu, M., Zhang, Z., Condon, A.: Secondary Structure Prediction of Interacting RNA Molecules. J. of Molecular Biology 345(5), 987-1001 (2005), www.rnasoft.ca/download.html
3. Arita, M., Kobayashi, S.: DNA Sequence Design Using Templates. New Generation Computing 20(3), 263-273 (2002)
4. Asahiro, Y.: Simple Greedy Methods for DNA Word Design. Proc. of 9th World Multi-Conference on Systemies, Cybernetics and Informatics 3, 186-191 (2005)
5. Braich, R., Chelyapov, N., Johnson, C., Rothemund, P., Adleman, L.: Solution of a 20-Variable 3-SAT Problem on a DNA Computer. Science 296(5567), 499-502 (2002)
6. Deaton, R., Kim, J., Chen, J.: Design and test of noncrosshybridizing oligonucleotide building blocks for DNA computers and nanostructures. Applied Physics Letters 82(8), 1305-1307 (2003)
7. Dirks, R., Lin, M., Winfree, E., Pierce, N.: Paradigms for computational nucleic acid design. Nucleic Acids Research 32(4), 1392-1403 (2004)
8. Faulhammer, D., Cukras, A., Lipton, R., Landweber, L.: Molecular computation: RNA solutions to chess problems. Proc. of the National Academy of Sciences of the United States of America 97(4), 1385-1389 (2000)
9. Garzon, M., Phan, V., Roy, S., Neel, A.: In Search of Optimal Codes for DNA Computing. In: Mao, C., Yokomori, T. (eds.) DNA Computing. LNCS, vol. 4287, pp. 143-156. Springer, Heidelberg (2006)
10. Kameda, A., Yamamoto, M., Ohuchi, A., Yaegashi, S., Hagiya, M.: Unravel Four Hairpins! In: Mao, C., Yokomori, T. (eds.) DNA Computing. LNCS, vol. 4287, pp. 381-392. Springer, Heidelberg (2006)
11. Kawshimo, S., Ono, H., Sadakane, K., Yamashita, M.: DNA Sequence Design by Dynamic Neighborhood Searches. In: Mao, C., Yokomori, T. (eds.) DNA Computing. LNCS, vol. 4287, pp. 157-171. Springer, Heidelberg (2006)
12. Lyngsø, R., Zuker, M., Pedersen, C.: Fast evaluation of internal loops in RNA secondary structure prediction. Bioinfomatics 15, 440-445 (1999)
13. Penchovsky, R., Ackermann, J.: DNA Library Design for Molecular Computation. J. of Computational Biology 10(2), 215-229 (2003)
14. Reif, J., Sahu, S., Yin, P.: Complexity of Graph Self-assembly in Accretive Systems and Self-destructible Systems. In: Carbone, A., Pierce, N.A. (eds.) DNA Computing. LNCS, vol. 3892, pp. 257-274. Springer, Heidelberg (2006)
15. Rose, J., Deaton, R., Suyama, A.: Statistical thermodynamic analysis and design of DNA-based computers. Natural Computing 3, 443-459 (2004)
16. Shiozaki, M., Ono, H., Sadakane, K., Yamashita, M.: A Probabilistic Model of DNA Conformational Change. In: Mao, C., Yokomori, T. (eds.) DNA Computing. LNCS, vol. 4287, pp. 274-285. Springer, Heidelberg (2006)
17. Shorteed, M., Chang, S., Hong, D., Phillips, M., Campion, B., Tulpan, D., Andronescu, M., Condon, A., Hoos, H., Smith, L.: A thermodynamic approach to designing struct-free combinatorial DNA word set. Nucleic Acids Research 33(15), 4965-4977 (2005)
18. Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Design of nucleic acid sequences for DNA computing based on a thermodynamic approach. Nucleic Acids Research 33(3), 903-911 (2005)
19. Tulpan, D., Hoos, H., Condon, A.: Stochastic Local Search Algorithms for DNA Word Design. In: Hagiya, M., Ohuchi, A. (eds.) DNA Computing. LNCS, vol. 2568, pp. 229-241. Springer, Heidelberg (2003)
20. Tulpan, D., Hoos, H.: Hybrid Randomized Neighborhoods Improve Stochastic Local Search for DNA Code Design. In: Xiang, Y., Chaib-draa, B. (eds.) Advances in Artificial Intelligence. LNCS (LNAI), vol. 2671, pp. 418-433. Springer, Heidelberg (2003)
21. Tulpan, D., Andronescu, M., Changf, S., Shortreed, M., Condon, A., Hoos, H., Smith, L.: Thermodynamically based DNA strand design. Nucleic Acids Research 33(15), 4951-4964 (2005)
22. Winfree, E., Liu, F., Wenzler, L., Seeman, N.: Design and self-assembly of DNA crystals. Nature 394, 539-544 (1998)
23. Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9, 133-148 (1981)