Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA)
Multiple Sequence Alignment (MSA) is one of the main topics in the bioinformatics domain, consists in finding an optimal alignment for three or more biological sequences with the number maximum of conserved zones or totally aligned columns. Different scores to assess the quality of the alignments hav...
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| Format: | Article |
| Language: | English |
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Escuela Politécnica Nacional (EPN)
2016-05-01
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| Series: | Latin-American Journal of Computing |
| Subjects: | |
| Online Access: | http://lajc.epn.edu.ec/index.php/LAJC/article/view/105 |
| _version_ | 1818316513856192512 |
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| author | Cristian Zambrano-Vega Miriam Cárdenas-Zea Ricardo Aguirre-Pérez |
| author_facet | Cristian Zambrano-Vega Miriam Cárdenas-Zea Ricardo Aguirre-Pérez |
| author_sort | Cristian Zambrano-Vega |
| collection | DOAJ |
| description | Multiple Sequence Alignment (MSA) is one of the main topics in the bioinformatics domain, consists in finding an optimal alignment for three or more biological sequences with the number maximum of conserved zones or totally aligned columns. Different scores to assess the quality of the alignments have been proposed, so the problem can be formulated and resolved as a Multi-Objective Optimization Problem (MOP). For this reason we have carried out a perfomanced study resolving the MSA problem under a multi-objective approach, considering two popular metrics as objectives to be optimized: The weighted Sum-Of-Pairs with affine gap penalties (wSOP) and the Totally Aligned Columns (TC), with three algorithms from the state-of- the-art of Multi-Objective Optimization: NSGAII, SPEA2 and MOCell. Our experiments reveals that the classic metaheuristic NSGA-II provides the best overall performance resolving some problems provided by the benchmark BAliBASE (v3.0), under a multi-objective and biological approach. |
| first_indexed | 2024-12-13T09:22:38Z |
| format | Article |
| id | doaj.art-80147cc7aaff43cf92411dd9daa75454 |
| institution | Directory Open Access Journal |
| issn | 1390-9266 1390-9134 |
| language | English |
| last_indexed | 2024-12-13T09:22:38Z |
| publishDate | 2016-05-01 |
| publisher | Escuela Politécnica Nacional (EPN) |
| record_format | Article |
| series | Latin-American Journal of Computing |
| spelling | doaj.art-80147cc7aaff43cf92411dd9daa754542022-12-21T23:52:41ZengEscuela Politécnica Nacional (EPN)Latin-American Journal of Computing1390-92661390-91342016-05-01314351Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA)Cristian Zambrano-Vega0Miriam Cárdenas-Zea1Ricardo Aguirre-Pérez2Universidad Técnica Estatal de QuevedoUniversidad Técnica Estatal de QuevedoUniversidad Técnica Estatal de QuevedoMultiple Sequence Alignment (MSA) is one of the main topics in the bioinformatics domain, consists in finding an optimal alignment for three or more biological sequences with the number maximum of conserved zones or totally aligned columns. Different scores to assess the quality of the alignments have been proposed, so the problem can be formulated and resolved as a Multi-Objective Optimization Problem (MOP). For this reason we have carried out a perfomanced study resolving the MSA problem under a multi-objective approach, considering two popular metrics as objectives to be optimized: The weighted Sum-Of-Pairs with affine gap penalties (wSOP) and the Totally Aligned Columns (TC), with three algorithms from the state-of- the-art of Multi-Objective Optimization: NSGAII, SPEA2 and MOCell. Our experiments reveals that the classic metaheuristic NSGA-II provides the best overall performance resolving some problems provided by the benchmark BAliBASE (v3.0), under a multi-objective and biological approach.http://lajc.epn.edu.ec/index.php/LAJC/article/view/105Multiple Sequence AlignmentMultiObjective Optimization MetaheuristicsoptimizationBioInformatics |
| spellingShingle | Cristian Zambrano-Vega Miriam Cárdenas-Zea Ricardo Aguirre-Pérez Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) Latin-American Journal of Computing Multiple Sequence Alignment MultiObjective Optimization Metaheuristics optimization BioInformatics |
| title | Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) |
| title_full | Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) |
| title_fullStr | Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) |
| title_full_unstemmed | Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) |
| title_short | Un enfoque Multi-Objetivo a la optimización del Alineamiento Múltiple de Secuancias (MSA) |
| title_sort | un enfoque multi objetivo a la optimizacion del alineamiento multiple de secuancias msa |
| topic | Multiple Sequence Alignment MultiObjective Optimization Metaheuristics optimization BioInformatics |
| url | http://lajc.epn.edu.ec/index.php/LAJC/article/view/105 |
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