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DNA Fragment Assembly by Ant Colony and Nearest Neighbour Heuristics

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Artificial Intelligence and Soft Computing – ICAISC 2006 (ICAISC 2006)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4029))

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Abstract

This paper presents the use of a combined ant colony system (ACS) and nearest neighbour heuristic (NNH) algorithm in DNA fragment assembly. The assembly process can be treated as combinatorial optimisation where the aim is to find the right order of each fragment in the ordering sequence that leads to the formation of a consensus sequence that truly reflects the original DNA strands. The assembly procedure proposed is composed of two stages: fragment assembly and contiguous sequence (contig) assembly. In the fragment assembly stage, a possible alignment between fragments is determined where the fragment ordering sequence is created using the ACS algorithm. The resulting contigs are then assembled together using the NNH rule. The results indicate that in overall the performance of the combined ACS/NNH technique is superior to that of a standard sequence assembly program (CAP3), which is widely used by many genomic institutions.

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References

  1. Applewhite, A.: Mining the genome. IEEE Spectrum 39(4), 69–71 (2002)

    Article  Google Scholar 

  2. Pop, M., Salzberg, S.L., Shumway, M.: Genome sequence assembly: Algorithms and issues. Computer 35(7), 47–54 (2002)

    Article  Google Scholar 

  3. Huang, X., Madan, A.: CAP3: A DNA sequence assembly program. Genome Research 9(9), 868–877 (1999)

    Article  Google Scholar 

  4. Green, P.: Phrap documentation. Phred, Phrap, and Consed (2004), http://www.phrap.org

  5. Ferreira, C.E., de Souza, C.C., Wakabayashi, Y.: Rearrangement of DNA fragments: A branch-and-cut algorithm. Discrete Applied Mathematics 116(1-2), 161–177 (2002)

    Article  MATH  MathSciNet  Google Scholar 

  6. Batzoglou, S., Jaffe, D., Stanley, K., Butler, J., Gnerre, S., Mauceli, E., Berger, B., Mesirov, J.P., Lander, E.S.: ARACHNE: A whole-genome shotgun assembler. Genome Research 12(1), 177–189 (2002)

    Article  Google Scholar 

  7. Kececioglu, J.D., Myers, E.W.: Combinatorial algorithms for DNA sequence assembly. Algorithmica 13(1-2), 7–51 (1995)

    Article  MATH  MathSciNet  Google Scholar 

  8. Pevzner, P.A., Tang, H., Waterman, M.S.: An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences of the United States of America 98(17), 9748–9753 (2001)

    Article  MATH  MathSciNet  Google Scholar 

  9. Burks, C., Engle, M., Forrest, S., Parsons, R., Soderlund, C., Stolorz, P.: Stochastic optimization tools for genomic sequence assembly. In: Adams, M.D., Fields, C., Venter, J.C. (eds.) Automated DNA Sequencing and Analysis, pp. 249–259. Academic Press, London (1994)

    Google Scholar 

  10. Parsons, R.J., Forrest, S., Burks, C.: Genetic algorithms, operators, and DNA fragment assembly. Machine Learning 21(1-2), 11–33 (1995)

    Article  Google Scholar 

  11. Parsons, R.J., Johnson, M.E.: A case study in experimental design applied to genetic algorithms with applications to DNA sequence assembly. American Journal of Mathematical and Management Sciences 17(3-4), 369–396 (1997)

    Google Scholar 

  12. Kim, K., Mohan, C.K.: Parallel hierarchical adaptive genetic algorithm for fragment assembly. In: Proceedings of the 2003 Congress on Evolutionary Computation, Canberra, Australia, pp. 600–607 (2003)

    Google Scholar 

  13. Angeleri, E., Apolloni, B., de Falco, D., Grandi, L.: DNA fragment assembly using neural prediction techniques. International Journal of Neural Systems 9(6), 523–544 (1999)

    Article  Google Scholar 

  14. Dorigo, M., Gambardella, L.M.: Ant colony system: A cooperative learning approach to the traveling salesman problem. IEEE Transactions on Evolutionary Computation 1(1), 53–66 (1997)

    Article  Google Scholar 

  15. Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. Journal of Molecular Biology 147(1), 195–197 (1981)

    Article  Google Scholar 

  16. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Research 33, D34–D38 (2005)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Research and Development Center for Intelligent Systems, King Mongkut’s Institute of Technology North Bangkok, 1518 Piboolsongkram Road, Bangsue, Bangkok, 10800, Thailand

    Wannasak Wetcharaporn & Nachol Chaiyaratana

  2. Institute of Field Robotics, King Mongkut’s University of Technology Thonburi, 91 Pracha u-tid Road, Bangmod, Thungkru, Bangkok, 10140, Thailand

    Nachol Chaiyaratana

  3. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Pathumthani, 12120, Thailand

    Sissades Tongsima

Authors
  1. Wannasak Wetcharaporn
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  2. Nachol Chaiyaratana
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  3. Sissades Tongsima
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Editor information

Editors and Affiliations

  1. Department of Artificial Intelligence, Academy of Humanities and Economics, Poland

    Leszek Rutkowski

  2. Institute of Automatics, AGH University of Science and Technology, Al. Mickiewicza 30, PL-30-059, Kraków, Poland

    Ryszard Tadeusiewicz

  3. Department of Electrical Engineering and Computer Sciences, Berkeley Initiative in Soft Computing (BISC), University of California, 94720-1776, Berkeley, CA, USA

    Lotfi A. Zadeh

  4. Department of Electrical Engineering, University of Louisville, 40292, Louisville, KY, U.S.A

    Jacek M. Żurada

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© 2006 Springer-Verlag Berlin Heidelberg

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Wetcharaporn, W., Chaiyaratana, N., Tongsima, S. (2006). DNA Fragment Assembly by Ant Colony and Nearest Neighbour Heuristics. In: Rutkowski, L., Tadeusiewicz, R., Zadeh, L.A., Żurada, J.M. (eds) Artificial Intelligence and Soft Computing – ICAISC 2006. ICAISC 2006. Lecture Notes in Computer Science(), vol 4029. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11785231_106

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  • DOI: https://doi.org/10.1007/11785231_106

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-35748-3

  • Online ISBN: 978-3-540-35750-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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