Related Experiment Video
Updated: Mar 18, 2026
Quantifying X-Ray Fluorescence Data Using MAPS
Published on: February 17, 2018
Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database
HaiXia Long1, ManZhi Li2, HaiYan Fu1
1School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China.
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.
