An Evolutionary Algorithm for the Maximum Weight Trace Formulation of the Multiple Sequence Alignment Problem
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.
Unable to display preview. Download preview PDF.
- 1.Chellapilla, K., Fogel, G.B.: Multiple sequence alignment using evolutionary programming. In: Angeline, P.J., et al. (eds.) Proceedings of the 1999 IEEE Congress on Evolutionary Computation, pp. 445–452. IEEE Press, Los Alamitos (1999)Google Scholar
- 5.Leopold, S.: An alignment graph based evolutionary algorithm for the multiple sequence alignment problem. Master’s thesis, Vienna University of Technology, Vienna, Austria (February 2004)Google Scholar
- 13.Zhang, C., Wong, A.K.C.: A genetic algorithm for multiple molecular sequence alignment. CABIOS 13(6), 565–581 (1997)Google Scholar