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Multi-level Ant Colony Optimization for DNA Sequencing by Hybridization

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Hybrid Metaheuristics (HM 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4030))

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Abstract

Deoxyribonucleic acid (DNA) sequencing is an important task in computational biology. In recent years the specific problem of DNA sequencing by hybridization has attracted quite a lot of interest in the optimization community. This led to the development of several metaheuristic approaches such as tabu search and evolutionary algorithms. In this work we propose an ant colony algorithm to resolve this problem. In addition, we apply our algorithm within a multi-level framework which helps in significantly reducing the computation time. The results show that our algorithm is currently among the state-of-the-art methods for this problem.

This work was supported by the Spanish CICYT project OPLINK (grant TIN-2005-08818-C04-01), and by the “Juan de la Cierva” program of the Spanish Ministry of Science and Technology of which Christian Blum is a post-doctoral research fellow.

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References

  1. Bains, W., Smith, G.C.: A novel method for nucleid acid sequence determination. Journal of Theoretical Biology 135, 303–307 (1988)

    Article  Google Scholar 

  2. Błażewicz, J., Formanowicz, P., Guinand, F., Kasprzak, M.: A heuristic managing errors for DNA sequencing. Bioinformatics 18(5), 652–660 (2002)

    Article  Google Scholar 

  3. Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., Weglarz, J.: DNA sequencing with positive and negative errors. Journal of Computational Biology 6, 113–123 (1999)

    Article  Google Scholar 

  4. Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., Weglarz, J.: Tabu search for DNA sequencing with false negatives and false positives. European Journal of Operational Research 125, 257–265 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  5. Błażewicz, J., Glover, F., Kasprzak, M.: DNA sequencing—Tabu and scatter search combined. INFORMS Journal on Computing 16(3), 232–240 (2004)

    Article  MathSciNet  Google Scholar 

  6. Błażewicz, J., Glover, F., Kasprzak, M.: Evolutionary approaches to DNA sequencing with errors. Annals of Operations Research 138, 67–78 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  7. Błażewicz, J., Kasprzak, M., Kuroczycki, W.: Hybrid genetic algorithm for DNA sequencing with errors. Journal of Heuristics 8, 495–502 (2002)

    Article  MATH  Google Scholar 

  8. Blum, C., Dorigo, M.: The hyper-cube framework for ant colony optimization. IEEE Transactions on Systems, Man, and Cybernetics – Part B 34(2), 1161–1172 (2004)

    Article  Google Scholar 

  9. Blum, C., Yábar Vallès, M.: New constructive heuristics for DNA sequencing by hybridization. Technical Report LSI-06-23-R, LSI, Universitat Politècnica de Catalunya, Barcelona, Spain (2006)

    Google Scholar 

  10. Brizuela, C.A., González, L.C., Romero, H.J.: An improved genetic algorithm for the sequencing by hybridization problem. In: Raidl, G.R., Cagnoni, S., Branke, J., Corne, D.W., Drechsler, R., Jin, Y., Johnson, C.G., Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G. (eds.) EvoWorkshops 2004. LNCS, vol. 3005, pp. 11–20. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  11. Bui, T.N., Youssef, W.A.: An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. In: Deb, K., et al. (eds.) GECCO 2004. LNCS, vol. 3103, pp. 908–919. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  12. Dorigo, M., Stützle, T.: Ant Colony Optimization. MIT Press, Boston (2004)

    Book  MATH  Google Scholar 

  13. Drmanac, R., Labat, I., Brukner, R., Crkvenjakov, R.: Sequencing of megabase plus DNA by hybridization: Theory of the method. Genomics 4, 114–128 (1989)

    Article  Google Scholar 

  14. Endo, T.A.: Probabilistic nucleotide assembling method for sequencing by hybridization. Bioinformatics 20(14), 2181–2188 (2004)

    Article  Google Scholar 

  15. Fernandes, E.R., Ribeiro, C.C.: Using an adaptive memory strategy to improve a multistart heuristic for sequencing by hybridization. In: Nikoletseas, S.E. (ed.) WEA 2005. LNCS, vol. 3503, pp. 4–15. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  16. Idury, R.M., Waterman, M.S.: A new algorithm for DNA sequence assembly. Journal of Computational Biology 2(2), 291–306 (1995)

    Article  Google Scholar 

  17. Lysov IuP, Y.P., Florentiev, V.L., Khorlin, A.A., Khrapko, K.R., Shik, V.V.: Determination of the nucleotide sequence of DNA using hybridization with oligonucleotides. a new method. Doklady Akademii nauk SSSR 303, 1508–1511 (1988)

    Google Scholar 

  18. Pevzner, P.A.: l-tuple DNA sequencing: Computer analysis. Journal of Biomulecular Structure and Dynamics 7, 63–73 (1989)

    Google Scholar 

  19. Walshaw, C.: Multilevel refinement for combinatorial optimization problems. Annals of Operations Research 131 (2004)

    Google Scholar 

  20. Walshaw, C., Cross, M.: Mesh partitioning: A multilevel balancing and refinement algorithm. SIAM Journal on Scientific Computing 22(1), 63–80 (2000)

    Article  MATH  MathSciNet  Google Scholar 

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Author information

Authors and Affiliations

  1. ALBCOM, Dept. Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, E-08034, Barcelona, Spain

    Christian Blum & Mateu Yábar Vallès

Authors
  1. Christian Blum
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  2. Mateu Yábar Vallès
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Editor information

Editors and Affiliations

  1. Department of Statistics and Computer Science, La Laguna University Spain,  

    Francisco Almeida

  2. Universitat Politècnica de Catalunya, Omega Campus Nord, Jordi Girona 1-3, 08034, Barcelona, Spain

    María J. Blesa Aguilera

  3. ALBCOM, Dept. Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain

    Christian Blum

  4. DEIOC, Universidad de La Laguna, Escuela Técnica Superior en Ingeniería Informática, Avda. Astrofísico Francisco Sánchez, s/n, 38271, La Laguna, Tenerife, Spain

    José Marcos Moreno Vega

  5. Escuela Técnica Superior en Ingeniería Informática, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez, s/n, 38271, La Laguna, Tenerife, Spain

    Melquíades Pérez Pérez

  6. DEIS, Campus of Cesena Alma Mater Studiorum, Università di Bologna, Cesena, Italy

    Andrea Roli

  7. Université Libre de Bruxelles, IRIDIA CP 194/6, Avenue Franklin D. Roosevelt 50, 1050, Bruxelles, Belgium

    Michael Sampels

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© 2006 Springer-Verlag Berlin Heidelberg

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Blum, C., Vallès, M.Y. (2006). Multi-level Ant Colony Optimization for DNA Sequencing by Hybridization. In: Almeida, F., et al. Hybrid Metaheuristics. HM 2006. Lecture Notes in Computer Science, vol 4030. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11890584_8

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  • DOI: https://doi.org/10.1007/11890584_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-46384-9

  • Online ISBN: 978-3-540-46385-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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