Degenerate primer design system for gene biodiversity study using dynamic pattern matching

Degenerate primer sets were designed to reveal biodiversity of genes using dynamic pattern matching. Bacterial nucleotide sequences were randomly selected from ten different genus and used to find universal primers for bacterial gene selection. Aligned sequences from different bacterial nucleotides were entered into the system consisted of three steps: data reformation, primer design, and property filtering. First, degenerate and consensus sequences were calculated using statistical models. The results were combined with Gibbs Free Energy to design and select the most appropriate sequences as a series of primer sets. Moreover, users can also adjust their own criteria for each primer set. The results indicate that the degenerate primers designed by our proposed system were proved to be positive.