Species Speci c Primer Design for Unique Identi cation of Closely Related Species

Abstract

Unique identi cation of closely related species is important when it comes to biomedi- cal and molecular biology research. For example Dengue virus has four serotypes(DEN-1, DEN-2, DEN-3 and DEN-4) and identifying the speci c serotype is important for its med- ical treatment. Conventional identi cation methods based on physiochemical properties could not uniquely distinguish each subtype due to the high degree of similarities in their interactions. DNA analysis can be employed for the purpose of unique identi cation, because of its capability to identify genetic information which makes one species di erent from another. Polymerase Chain Reaction(PCR) is a technique which has been proven to be e cient in DNA analysis of closely-related species. The primary requirement of PCR is a pair of special DNA fragments called "primers" which are used to mark the DNA fragment of interest. However, to use PCR for this purpose, we need to design primers which mark unique DNA fragment(s) of a species which can distinguish it from the rest of the closely- related species. This research focuses on nding a computational method to generate species-speci c unique primers. PCR experiments could possibly fail due to several reasons such as self-dimer and hair- pin formation. Recent research from other classes of primer design (eg. general primer design, conserved primer design) have addressed this issue by using computational primer validation methods. We have extended this concept in our research to introduce a compu- tational primer validation method based on Fuzzy-Adaptive Particle Swarm Optimization (FAPSO) for the class of "species-speci c" primer design. Considering the requirements of unique primer design as well as experimental needs of PCR, we propose an overall design of a possible tool that can be implemented to gen- erate unique primers. Moreover, to validate our design, we have built a prototype by manipulating existing tools and algorithms according to our overall design. Considering the requirement of using resultant primers of a possible tool directly to a "wet-lab" ex- periment, we introduce a thorough evaluation scheme to evaluate a primer design tool of this kind. Based on the evaluation results of the primers generated by our prototype for serotypes of Dengue, we have identi ed that primers generated by our method can be directly used for a wet-lab experiment as the quality is higher than the primers generated by pre- existing methods.