An efficient rank based approach for closest string and closest substring

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Dinu, Liviu P ^a   Ionescu, Radu ^a  

^a UNIVERSITY OF BUCHAREST   (Romania)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; COW; DNA SEQUENCE; DONKEY; DORMOUSE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC PARAMETERS; GORILLA; HAMMING DISTANCE; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; INTERMETHOD COMPARISON; LEVENSHTEIN DISTANCE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; RAT; TAXONOMIC RANK; ALGORITHM; ANIMAL; BIOLOGY; CHROMOSOME; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

ALGORITHMS; ANIMALS; BASE SEQUENCE; CHROMOSOMES, MAMMALIAN; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT;

EID: 84861899035     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037576     Document Type: Article

References (34)

1. Liew AWC, Yan H, Yang M, (2005) Pattern recognition techniques for the emerging field of bioinformatics: A review. Pattern Recognition, 38: 2055-2073.
2. Lanctot K, Li M, Ma B, Wang S, Zhang L, (2003) Distinguishing String Selection Problems. 2003 Information and Computation, 185 41-55. A preliminary version appeared in Proceedings of 10th ACM-SIAM Symposium on Discrete Algorithms, 633-642,.
3. Gramm J, Huffner F, Niedermeier R, (2002) Closest Strings, Primer Design, and Motif Search. Currents in Computational Molecular Biology, poster abstracts of RECOMB 2002 74-75 pp. 74-75.
4. Deng X, Li G, Li Z, Ma B, Wang L, (2003) Genetic Design of Drugs without Side-Effects. SIAM Journal on Computing, 32: 1073-1090.
5. Ben-Dor A, Lancia G, Perone J, Ravi R, (1997) Banishing Bias from Consensus Sequences. In Proceedings of CPM, Lecture in Computer Science, 1264: 247-261.
6. Wang L, Dong L, (2005) Randomized Algorithms for Motif Detection. Journal of Bioinformatics and Computational Biology, 3: 1038-1052.
7. Li M, Ma B, Wang L, (2002) Finding Similar Regions in Many Sequences. 1999 Journal of Comput. Syst. Sci., 65 111-132. A preliminary version appeared in Proceedings of the 31st ACM Symposium on Theory of Computing, 473-482,.
8. Roman S, (1992) Coding and Information Theory. Graduate Texts in MathematicsSpringervol 134 ‰.
9. Koonin EV, (1999) The emerging paradigm and open problems in comparative genomics. Bioinformatics, 15: 265-266.
10. Wooley JC, (1999) Trends in computational biology: a summary based on a RECOMB plenary lecture. Journal of Computational Biology, 6: 459-474.
11. Levenshtein VI, (1966) Binary codes capable of correcting deletions, insertions and reverseals. Cybernetics and Control Theory, 10 (8): 707-710.
12. Palmer J, Herbon L, (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. Journal of Molecular Evolution, 28: 87-89.
13. Dinu LP, (2003) On the classification and aggregation of hierarchies with different constitutive elements. Fundamenta Informaticae, 55 (1): 39-50.
14. Dinu LP, Sgarro A, (2006) A Low-complexity Distance for DNA Strings. Fundamenta Informaticae, 73 (3): 361-372.
15. Dinu A, Dinu LP, (2005) On the Syllabic Similarities of Romance Languages. In Proceedings of CICLingvol. 3406 of LNCS pp. 785-788.
16. Dinu LP, Popescu M, Dinu A, (2008) Authorship Identification of Romanian Texts with Controversial Paternity. In Proceedings of LREC.
17. Dinu LP, Manea F, (2006) An Efficient Approach for the Rank Aggregation Problem. Theoretical Computer Science vol. 359 (1-3): 455-461.
18. Frances M, Litman A, (1997) On Covering Problems of Codes. Theory Comput. Syst 30 (2): 113-119.
19. Chimani M, Woste M, Bocker S, (2011) A Closer Look at the Closest String and Closest Substring Problem. In Proceedings of ALENEXpp. 13-24.
20. Karpovsky M, (1981) Weight Distribution of Translates, Covering Radius and Perfect Codes. IEEE Trans. Inform. Theory, vol. IT-27: 462-472.
21. Liu X, He H, Skora O, (2005) Parallel genetic algorithm and parallel simulated annealing algorithm for the closest string problem. In Proceedings of ADMAvol. 3584 of LNCS pp. 591-597.
22. de la Higuera C, Casacuberta F, (2000) Topology of strings: Median string is NP-complete. Theoretical Computer Science, 230: 39-48.
23. States DJ, Agarwal P, (1996) Compact encoding strategies for DNA sequence similarity search. In Proceedings of the 4th International Conference on Intelligent Systems for Molecular BiologyAAAI Press pp. 211-217.
24. Nicolas F, Rivals E, (2003) Complexities of centre and median string. LNCS vol. 2676: 315-327.
25. Nicolas F, Rivals E, (2005) Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances. Journal of Discrete Algorithms, 3 (2-4): 390-415.
26. Popov VY, (2007) Multiple genome rearrangement by swaps and by element duplications. Theoretical Computer Science, 385 (1-3): 115-126.
27. Dinu LP, Popa A, (2012) On the closest string via rank distance. In Proceedings of CMPvol. 7354 of LNCS pp. 413-426.
28. Diaconis P, Graham RL, (1977) Spearman footrule as a Measure of Disarray. Journal of Royal Statistical Society. Series B (Methodological), 39 (2): 262-268.
29. Dinu LP, Ionescu R, (2011) A genetic approximation for closest string via rank distance. In Proceedings of 13th Symposium on Symbolic and Numeric Algorithms for Scientific Computing pp. 207-215.
30. Holmquist R, Miyamoto M, Goodman M, (1988) Higher-Primate Phylogeny- Why Can't We Decide? Mol. Biol. Evol., 5 (3): 201-216.
31. Banzhaf W, Nordin P, Keller R, Francone F, (1998) Genetic Programming- An Introduction. Morgan Kaufmann San Francisco, CA.
32. Schmitt L, (2001) Theory of Genetic Algorithms. Theoretical Computer Science 259: 1-61.
33. Fraser AS, (1957) Simulation of Genetic Systems by Automatic Digital Computers. I. Introduction. Australian Journal of Biological Sciences 10: 484-491.
34. Fraser AS, Burnell D, (1970) Computer Models in Genetics. New York McGraw-Hill.