A Graph-Based Genetic Algorithm for the Multiple Sequence Alignment Problem
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.
KeywordsMultiple Sequence Alignment Memory Complexity Progressive Alignment 27th Annual International Confer Multiple Sequence Alignment Algorithm
Unable to display preview. Download preview PDF.
- 5.Leach, A.R.: Molecular Modelling: Principles and Applications, 2nd edn. Prentice-Hall, Englewood Cliffs (2001)Google Scholar
- 6.Lopes, H.S., Moritz, G.L.: A distributed approach for multiple sequence alignment using a parallel virtual machine. In: Proc. 27th Annual International Conference of IEEE EMBS, Shanghai, China (2005)Google Scholar