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Volume: 3 Issue: 2

Multiple sequence alignment using swarm intelligence

Pedro F. Rodriguez, Luis F. Niño, Oscar M. Alonso

Abstract:
In this work, a novel approach to multiple sequence alignment based on Particle Swarm Optimization (PSO) is introduced. The proposed approach tries to improve a sequence alignment previously obtained using Clustal X. Special representation and operators are designed to deal with the sequence alignment problem. Some experiments over families of proteins were carried out in order to test the proposed approach. In most cases, the PSO algorithm was able to improve the starting alignment obtained using Clustal X.

Keywords:
swarm intelligence, sequence alignment, bioinformatics

doi:10.5019/j.ijcir.2004.96

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