An Evolutionary Algorithm for the Maximum Weight Trace Formulation of the Multiple Sequence Alignment Problem

  • Gabriele Koller
  • Günther R. Raidl
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3242)

Abstract

The multiple sequence alignment problem (MSA) can be re-formulated as the problem of finding a maximum weight trace in an alignment graph, which is derived from all pairwise alignments. We improve the alignment graph by adding more global information. A new construction heuristic and an evolutionary algorithm with specialized operators are proposed and compared to three other algorithms for the MSA, indicating the competitiveness of the new approaches.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Gabriele Koller
    • 1
  • Günther R. Raidl
    • 1
  1. 1.Institute of Computer Graphics and AlgorithmsVienna University of TechnologyViennaAustria

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