Multithreaded Parallel Sequence Alignment Based on Needleman-Wunsch Algorithm

Biocomputing and molecular biology are areas that change knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This requires the utilization of high performance computers and innovative software tools for management of the vast information, as well as deployment of innovative algorithmic techniques for analysis, interpretation and prognostication of data in order to get to insight of the design and validation of life-science experiments. Sequence alignment is an important method in DNA and protein analysis. The paper describes the computational challenges in biological sequence processing. The great challenges are to propose parallel computational models and parallel program implementations based on the algorithms for biological sequence alignment. An investigation of the efficiency of sequence alignment based on parallel multithreaded program implementation of Needleman-Wunsch algorithm is presented in this paper. Parallel computational model based on Needleman-Wunsch algorithm is designed. The proposed parallel model is verified by multithreaded parallel program implementation utilizing OpenMP. A number of experiments have been carried out for the case of various data sets and a various number of threads. Parallel performance parameters execution time and speedup are estimated experimentally. The performance estimation and scalability analyses show that the suggested model has good scalability both in respect to the workload and machine size.