Fast exact sequence alignment using parallel computing

Abstract

Bioinformatics is a growing field that attracts many researchers and continues to prove its value and significance. Since the early days of discovering genomic martial and using it to identify new life forms, sequence alignment applications have become important in enabling discoveries of important biological or medical benefits. Finding similarities, or even relations between sequences, is a demanding process that requires time and high cost. However, nowadays there are plenty of algorithms that are used to find similarity and/or differences between sequences. Many of these algorithms still suffer from performance issues, such as slow performance and poor scalability. Therefore, parallelization is widely used to address these issues. In this paper, we utilize a multi-threading parallelism technique coupled with a block alignment idea in order to improve the sequence alignment performance. The experiments show that the proposed implementation outperforms the sequential implementation by 4.9 times for sequences of lengths ranging between 1024 and 8192.