Optimizing Unique Sequence Identification for Polymerase Chain Reaction Primer Design

Abstract

Polymerase Chain Reaction is a biochemical reaction that enables the amplification of selected regions of DNA strands. This is done by designing primers that anneal to the strand at specific positions, for this to happen as expected the primers must be unique to the DNA sequences considered. Finding unique subsequences for making primers has been a problem addressed by researchers from fields of computer science and bioinformatics. We explore opportunities to make the process of picking primers faster by proposing a fast and memory efficient algorithm that can pick unique subsequences of a given set of DNA sequences. We introduce the two novel algorithms, SWHASH and OSAS. One optimized for larger input sizes and the other for smaller inputs. OSAS was built on the proven correctness of Suffix Array Sorting. SWHASH was tested against the results taken from OSAS. And we have proven empirically that the loss rates for generic DNA sequence inputs are below 10% most of the time.