Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-Conquer

  • Yixin Chen
  • Yi Pan
  • Juan Chen
  • Wei Liu
  • Ling Chen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3992)


Multiple sequence alignment is a common task in molecular biology and bioinformatics. Obtaining an accurate alignment of protein sequences is a difficult computational problem because many heuristic techniques cannot achieve optimality in a reasonable running time. A novel multiple sequence alignment algorithm based on ant colony optimization and divide-and-conquer technique is proposed. The algorithm divides a set of sequences into several subsections vertically by bisecting the sequences recursively using the ant colony optimization method. We also present two methods that adaptively adjust the parameters and update the pheromones to avoid local optimal traps. Experimental results show that the algorithm can achieve high quality solution and significantly reduce the running time.


Multiple Sequence Alignment High Quality Solution Frequency Assignment Problem Sequence Alignment Method Future Generation Computer System 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Yixin Chen
    • 1
  • Yi Pan
    • 2
  • Juan Chen
    • 3
  • Wei Liu
    • 3
  • Ling Chen
    • 3
  1. 1.Department of Computer ScienceWashington University in St. LouisSt. LouisUSA
  2. 2.Department of Computer ScienceGeorgia State UniversityAtlantaUSA
  3. 3.Department of Computer ScienceYangzhou UniversityYangzhouChina

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