Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database

BACKGROUND: Multiple sequence alignment (MSA) is one of the most important research contents in bioinformatics. A number of MSA programs have emerged. The accuracy of MSA programs highly depends on the parameters setting, mainly including gap open penalties (GOP), gap extension penalties (GEP) and s...

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Detalles Bibliográficos
Autores principales: Long, HaiXia, Li, ManZhi, Fu, HaiYan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2016
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909661/
https://www.ncbi.nlm.nih.gov/pubmed/27376004
http://dx.doi.org/10.1186/s40064-016-2526-5
Descripción
Sumario:BACKGROUND: Multiple sequence alignment (MSA) is one of the most important research contents in bioinformatics. A number of MSA programs have emerged. The accuracy of MSA programs highly depends on the parameters setting, mainly including gap open penalties (GOP), gap extension penalties (GEP) and substitution matrix (SM). This research tries to obtain the optimal GOP, GEP and SM rather than MAFFT default parameters. RESULTS: The paper discusses the MAFFT program benchmarked on BAliBASE3.0 database, and the optimal parameters of MAFFT program are obtained, which are better than the default parameters of CLUSTALW and MAFFT program. CONCLUSIONS: The optimal parameters can improve the results of multiple sequence alignment, which is feasible and efficient.

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