A Graph-Based Genetic Algorithm for the Multiple Sequence Alignment Problem

  • Heitor S. Lopes
  • Guilherme L. Moritz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4029)


We developed a new approach for the multiple sequence alignment problem based on Genetic Algorithms (GA). A new method to represent an alignment is proposed as a multidimensional oriented graph, which dramatically decreases the storage complexity. Details of the proposed GA are explained, including new structure-preserving genetic operators. A sensitivity analysis was done for adjusting running parameters of the GA. Performance of the proposed system was evaluated using a benchmark of hand-aligned sequences (Balibase). Overall, the results obtained are comparable or better to those obtained by a well-known software (Clustal). These results are very promising and suggest more efforts for further developments.


Multiple Sequence Alignment Memory Complexity Progressive Alignment 27th Annual International Confer Multiple Sequence Alignment Algorithm 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Heitor S. Lopes
    • 1
  • Guilherme L. Moritz
    • 1
  1. 1.Bioinformatics LaboratoryCPGEI, Federal Technological University of ParanáCuritibaBrazil

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