Developing New Pairwise Sequence Alignment Method Based on Needleman-Wunsch Algorithm

Abstract

Molecular biology and bioinformatics are fields that alter knowledge and abilities for gathering, managing, storing, analyzing, interpreting, and disseminating biological data. In order to get insight into the design and testing of life sciences, it is necessary to make use of high-performance computers, cutting-edge software tools, and unique algorithmic approaches for data analysis, interpretation, and prognostication. The computing challenges of processing biological sequences are used in this research to describe a significant technique for producing DNA sequence alignments. One of these challenges is to put forward computational models that aid in speeding up the computation of the substitution matrix of the needleman-wunsch algorithm. Another difficulty is the implementation of a parallel program for two threads to find the values of the matrix concurrently in order to achieve high efficiency and find the best sequence alignment in less time. This paper introduces a novel approach to constructing the substitution matrix of the Needleman-Winch algorithm. This approach enhances the overall performance of the algorithm by adjusting the values of the penalties imposed for the gap, mismatch, and match in addition to computing the matrix using two parallel threads depending on the progress made in the devices, especially with regard to the capabilities and performance of the GPU. Numerous tests have been run using different data sets and different lengths of sequence. A comparison was made between the amount of time needed to implement the Needleman method and the amount of time needed to implement the suggested model using the same data in order to evaluate the performance of the proposed model. Processing time and speedup for parallel performance are experimentally calculated. The recommended model has high scalability in terms of workload and machine capacity, according to the performance evaluation and scalability assessments. The proposed approach reduced the execution time ratio by 47% to 90%, and this improvement rate rises as the length of the reference and query sequences does.