Solving Computationally Intensive Problem Using GPUs- Solving Motif Finding Problem as a Case Study

Abstract

With scientific problems getting larger and more complicated, level of parallelization needed to be increased to provide the needed amount of computational power, so more adequate, efficient and robust parallel environments became an essential need for scientific research. This thesis proposes hybrid parallel paradigms to solve computationally intensive problem, taking into consideration one of the most common problems in Bioinformatics, Motif Finding as a case study. Motifs are defined as the short patterns these consist of nucleotide; they are usually positioned close to the genes contained in Deoxyribo Nucleic Acid (DNA). They occur in a frequent manner within the sequence, these patterns are not identical but it comes with some mutations in several of their nucleotide positions. Motif Finding Problem aims to discover unknown motifs that are expected to be common in a set of sequences. Generally it can be viewed as a large-length sequence matching problem.