High-accuracy alignment of sequences with disease information contributes to disease treatment and prevention. The results\nof multiple sequence alignment depend on the parameters of the objective function, including gap open penalties (GOP), gap\nextension penalties (GEP), and substitution matrix (SM). Firstly, the theory parameter formulas relating to GOP, GAP, and SMare\ninferred, combining unaligned sequence length, number, and identity. Secondly, we tested the rationality of the theory parameter\nformulas, with experiment on the ClustalW and MAFFT program. In addition,we obtained a group of MAFFT programparameters\naccording to the formulas proposed. The results of all experiments show that the SPS (sum-of-pair score) obtained from theory\nparameters is better than the SPS obtained from the default parameters of ClustalW and MAFFT. In both theory and practice,\nour method to determine the parameters is feasible and efficient. These can provide high-accuracy alignment results for precision\nmedicine.
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