Application And Implementation Of Parallel Computing In Bioinformatics

Bioinformatics is a multi-discipline cross-cutting and the formation of a new subject, is the core of life science and science fields and one of the most dynamic frontier of today. Using computer systems for scientific computing and simulation has become the most important method in modern biological research. In bioinformatics, DNA sequence alignment and assembly, gene expression data analysis are the most common and important contents, they require high performance computers for the amount of data analysis and calculations. Although the high-performance parallel computers meet the needs of large-scale computing, they are so expensive that many research institutions and universities cannot afford. In this paper we developed a platform for parallel computing in bioinformatics with the help of the PC-LAN.We constructed a scalable architecture model called Bio_Mpi. After analyzing the existing software phrap, a new parallel algorithm was presented. Based on this algorithm, a parallel software package named mpiphrap was developed. Three softwares, including mpiphrap, mpiblast and HMMER were transplanted to Bio_Mpi framework.Finally, given a single node and multi-node operating environment, mpiphrap, mpiblast and HMMER were tested respectively. The testing results indicate that mpiphrap, mpiblast and HMMER are efficient and feasible.