Single RNA Secondary Structure Prediction based Dynamical programming algorithms: to parallelize or not?

Abstract

RNA Secondary Structure Prediction has a huge importance for Bioinformatics. Over the last decade, Dynamical Algorithms used for that purpose reached performance bottlenecks, with data produced by RNA sequences. The main idea of this paper is to answer the question – to parallelize or not? We aim to achieve a better performance over different algorithms. The chronological development of algorithms is followed and we try to obtain better execution time accordingly, where we introduce comparison between serial and parallel version of the algorithm. As a performance measurements are obtained the Time Complexity and Accuracy Level with accent on the best algorithm for the purpose needed.