Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

Computational Biology and Chemistry

Volumn 28, Issue 1, 2004, Pages 11-19

  Błzewicz, Jacek ^a,b   Formanowicz, Piotr ^a,b   Kasprzak, Marta ^a,b   Markiewicz, Wojciech T ^b   Świercz, Aleksandra ^a  

^a POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

Heuristics; Isothermic libraries; Sequencing by hybridization; Tabu search

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; ERROR ANALYSIS; GENETIC ENGINEERING; POLYNOMIALS; PROBLEM SOLVING; THERMAL EFFECTS;

HEURISTICS; ISOTHERMIC LIBRARIES; SEQUENCING BY HYBRIDIZATION (SBH); TABU SEARCH;

DNA SEQUENCES;

OLIGONUCLEOTIDE;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; GENE LIBRARY; GENETICS; HYBRIDIZATION; NUCLEOTIDE SEQUENCE; TEMPERATURE;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE LIBRARY; HYBRIDIZATION, GENETIC; OLIGONUCLEOTIDES; TEMPERATURE;

EID: 12144287366     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2003.12.002     Document Type: Article

References (28)

1. Bains W., Hybridization methods for DNA sequencing. Genomics. 11:1991;294-301.
2. Bains W., Smith G.C., A novel method for nucleic acid sequence determination. J. Theor. Biol. 135:1988;303-307.
3. Błażewicz, J., Kasprzak M., Complexity of DNA sequencing by hybridization. Theor. Comput. Sci. 290:2002;1459-1473.
4. Błażewicz, J., Kaczmarek J., Kasprzak M., Markiewicz W.T., Wȩglarz J., Sequential and parallel algorithms for DNA sequencing. CABIOS. 13:1997;151-158.
5. Błażewicz, J., Formanowicz P., Kasprzak M., Markiewicz W.T., Wȩglarz J., DNA sequencing with positive and negative errors. J. Comp. Biol. 6:1999;113-123.
6. Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., 2000a. Isothermic oligonucleotide libraries. In: Miyano, S., Shamir, R., Takagi, T. (Eds.), Currents in Computational Molecular Biology, pp. 97-98.
7. Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., 2000b. Sequencing by hybridization with isothermic oligonucleotide libraries. Research report RA-002/2000, Poznań Supercomputing and Networking Center, in press.
8. Błażewicz, J., Formanowicz P., Kasprzak M., Markiewicz W.T., Wȩglarz J., Tabu search for DNA sequencing with false negatives and false positives. Eur. J. Oper. Res. 125:2000;257-265.
9. Drmanac R., Labat I., Brukner I., Crkvenjakov R., Sequencing of megabase plus DNA by hybridization: theory and the method. Genomics. 4:1989;114-128.
10. Fodor S.P.A., Read J.L., Pirrung M.C., Stryer L., Lu A., Solas D., Light-directed, spatially addressable parallel chemical synthesis. Science. 251:1991;767-773.
11. Fogel, G.B., Chellapilla, K., 1999. Simulated sequencing by hybridization using evolutionary programming. In: Proceedings of the IEEE Congress in Evolutionary Computations (CEC'99), IEEE Service Center, Piscatawag, pp. 445-452.
12. Fogel G.B., Chellapilla K., Fogel D.B., Reconstruction of DNA sequence information from a simulated DNA chip using evolutionary programming. Lect. Notes Comput. Sci. 1447:1998;429-436.
13. Gallant J., Maier D., Storer J.A., On finding minimal length superstrings. J. Comput. Syst. Sci. 20:1980;50-58.
14. Glover, F., Laguna, M., 1997. Tabu Search. Kluwer Academic Publishers, Boston.
15. Guénoche A., Can we recover a sequence, just knowing all its subsequences of given length? CABIOS. 8:1992;569-574.
16. Halperin, E., Halperin, S., Hartman, T., Shamir, R., 2002. Handling long targets and errors in sequencing by hybridization. In: Proceedings of the 6th RECOMB, pp. 176-185.
17. Khrapko K.R., Lysov Y.P., Khorlin A.A., Shik V.V., Florentiev V.L., Mirzabekov A.D., An oligonucleotide approach to DNA sequencing. FEBS Lett. 256:1989;118-122.
18. Lipshutz R.J., Likelihood DNA sequencing by hybridization. J. Biomol. Struct. Dyn. 11:1993;637-653.
19. Needleman S.B., Wunsch C.D., A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453.
20. Pease A.C., Solas D., Sullivan E., Cronin M., Holmes C., Fodor S., Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. U.S.A. 91:1994;5022-5026.
21. Pevzner P.A., l-Tuple DNA sequencing: computer analysis. J. Biomol. Struct. Dyn. 7:1989;63-73.
22. Pevzner, P.A., Lipshutz, R.J., 1994. Towards DNA sequencing chips. In: Prívara, I., Rovan, B., Ružička, P. (Eds.), Mathematical Foundations of Computer Science 1994. Springer-Verlag, Berlin, pp. 143-158.
23. Phan V.T., Skiena S.S., Dealing with errors in interactive sequencing by hybridization. Bioinformatics. 17:2001;862-870.
24. Shamir R., Tsur D., Large scale sequencing by hybridization. J. Comp. Biol. 9:2002;413-428.
25. Southern, E.M., 1988. UK Patent Applic. GB8 810400.
26. Southern E.M., Maskos U., Elder J.K., Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 13:1992;1008-1017.
27. Wallace R.B., Johnson M.J., Hirose T., Miyake T., Kawashima E.H., Itakura K., The use of synthetic oligonucleotides as hybridization probes. II. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA. Nucleic Acids Res. 9:1981;879-894.
28. Zhang J., Wu L., Zhang X., Reconstruction of DNA sequencing by hybridization. Bioinformatics. 19:2002;14-21.