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

HaiXia Long; ManZhi Li; HaiYan Fu

doi:10.1186/s40064-016-2526-5

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

Springerplus. 2016 Jun 16;5(1):736. doi: 10.1186/s40064-016-2526-5. eCollection 2016.

Authors

HaiXia Long¹, ManZhi Li², HaiYan Fu¹

Affiliations

¹ School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China.
² School of Mathematics and Statistics, Hainan Normal University, Haikou, 571158 HaiNan China.

Abstract

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.

Keywords: Default parameters; Gap extension penalties; Gap open penalties; MAFFT program; Multiple sequence alignment; Substitution matrix.