Physical Mapping Using Simulated Annealing and Evolutionary Algorithms

Research output: Contribution to book/anthology/report/proceedingBook chapterResearch

  • Jacob Svaneborg Vesterstrøm, Denmark
  • Department of Computer Science
Physical mapping (PM) is a method of bioinformatics that assists in DNA sequencing. The goal is to determine the order of a collection of fragments taken from a DNA strand, given knowledge of certain unique DNA markers contained in the fragments. Simulated annealing (SA) is the most widely used optimization method when searching for an ordering of the fragments in PM. In this paper, we applied an evolutionary algorithm to the problem, and compared its performance to that of SA and local search on simulated PM data, in order to determine the important factors in finding a good ordering of the segments. The analysis highlights the importance of a good PM model, a well-correlated fitness function, and high quality hybridization data. We suggest that future work in PM should focus on design of more reliable fitness functions and on developing error-screening algorithms.
Original languageEnglish
Title of host publicationProceedings of the IEEE Congress on Evolutionary Computation, CEC 2003, 8 -12 December 2003, Canberra, Australien
Number of pages7
Volume1
Place of publicationdblp.uni-trier.de
PublisherIEEE Press
Publication year2003
Pages327- 334
ISBN (print)0-7803-7804-0
ISBN (Electronic)10.1109/CEC.2003.1299593
Publication statusPublished - 2003

    Research areas

  • DNA, biological computing, evaluationary computing, search problems, simulated annealing

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