ArticleSpringerPlus2016
Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database.
Article in SpringerPlus, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Much ado about nothing: modeling amino acid replacement with predicted protein structures.Bioinformatics (Oxford, England) · 2026Article
- The Evolution of Function in the DNA-Binding Domain of the CRP/FNR Family.Genome biology and evolution · 2025Article
- DiMA: sequence diversity dynamics analyser for viruses.Briefings in bioinformatics · 2024Article
- An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.Methods in molecular biology (Clifton, N.J.) · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMultiple 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.
resultsThe 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.
conclusionsThe optimal parameters can improve the results of multiple sequence alignment, which is feasible and efficient.
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