Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns

• DOI: 10.1093/bioinformatics/btt360
• Publication Date: 2013-06-23T00:20:14Z
• Authors: Francisco M. Ortuño; Olga Valenzuela; Fernando Rojas; Hector Pomares; Javier P. Florido; Jose M. Urquiza; Ignacio Rojas
• Keywords: Multiple sequence alignment; Alignment-free sequence analysis; Benchmark (surveying); Sequence (biology)

Abstract Motivation: Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, each one is focused on specific features. Thus, the same set of sequences can produce different above all when less similar. Consequently, researchers and biologists do not agree about which most suitable way evaluate MSAs. Recent evaluations tend use more complex scores including further Among them, 3D structures increasingly being alignments. Because conserved proteins than sequences, with structural information better suited distant relationships between sequences. Results: The proposed multiobjective algorithm, based non-dominated sorting genetic aims jointly optimize three objectives: STRIKE score, non-gaps percentage totally columns. It was significantly assessed BAliBASE benchmark according Kruskal–Wallis test (P < 0.01). This algorithm also outperforms aligners, ClustalW, Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence (PIMA), MULTIALIGN, (SAGA), PILEUP, Rubber Band Technique (RBT-GA) Vertical Decomposition (VDGA), Wilcoxon signed-rank 0.05), whereas it shows results 3D-COFFEE > 0.05) advantage able structures. Structural included within objective accurately obtained Availability: source code available at http://www.ugr.es/∼fortuno/MOSAStrE/MO-SAStrE.zip. Contact: [e-mail] Supplementary Information: material Bioinformatics online.