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

Abstract

Degenerate primer design for studying biodiversity is a difficult step in molecular biology. The primers must be specific to the gene. Choosing the right primers are somewhat difficult and sometimes led to mismatching. Several primer design systems have been developed to overcome this problem. In this study, the Dynamic Pattern Matching technique has been developed and applied to find bacterial universal primers and specific primers for Glycoside Hydrolase Family 45 genes. Aligned sequences from test sets are entered into the system which consists of three steps: data reformation, primer design, and property filtering. First, degenerate and consensus sequences are calculated using statistical models. The results are 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 are proved to be positive.