Abstract: Dynamic programming is one of the most popular methods in bioinformatics. Many bioinformatics problems, such as
sequence comparison, gene recognition, protein sequence rearrangement, and protein structure and function analysis, can be solved by
dynamic programming, but dynamic programming consumes too much time, so it is generally used to solve double sequence alignment
problems. In this paper, by analyzing the characteristics of sequence alignment and combining with the idea of dynamic programming
method, the homologous DNA double sequence alignment using dynamic programming method is realized. The specific process of
comparison is given, and the implementation steps of the algorithm are listed.

Key words: sequence alignment, dynamic programming, optimal substructure properties, optimal alignment