This invention relates to the interdisciplinary field of
molecular biology and
bioinformatics, specifically to a method and
system for designing multi-site
mutation primers based on rule constraints and multi-objective optimization. The method includes the following steps: receiving the target
DNA sequence and
mutation site information; automatically grouping the
mutation sites according to their position distribution and spacing in the
DNA sequence; determining the corresponding primer design region by extending a
fixed length upstream and downstream from the center position of each mutation group; generating multiple candidate primer sequences based on the primer design region using a sliding window method; constructing a multi-objective optimization scoring function based on annealing temperature,
GC content, and primer length to comprehensively
score and screen the candidate primers to obtain the optimal primer; optimizing the 3' end of the optimal primer to preferentially contain stable bases; and outputting the optimized primer sequence and related design parameters and explanation information, effectively solving the pain points of existing multi-site mutation primer designs.