title: An improved distance matrix computation algorithm for multicore clusters.
abstract: Distance matrix has diverse usage in different research areas. Its computation is typically an essential task in most bioinformatics applications, especially in multiple sequence alignment. The gigantic explosion of biological sequence databases leads to an urgent need for accelerating these computations. DistVect algorithm was introduced in the paper of Al-Neama et al. (in press) to present a recent approach for vectorizing distance matrix computing. It showed an efficient performance in both sequential and parallel computing. However, the multicore cluster systems, which are available now, with their scalability and performance/cost ratio, meet the need for more powerful and efficient performance. This paper proposes DistVect1 as highly efficient parallel vectorized algorithm with high performance for computing distance matrix, addressed to multicore clusters. It reformulates DistVect1 vectorized algorithm in terms of clusters primitives. It deduces an efficient approach of partitioning and scheduling computations, convenient to this type of architecture. Implementations employ potential of both MPI and OpenMP libraries. Experimental results show that the proposed method performs improvement of around 3-fold speedup upon SSE2. Further it also achieves speedups more than 9 orders of magnitude compared to the publicly available parallel implementation utilized in ClustalW-MPI.
authors.affiliation: Department of Mathematics, Faculty of Science, Al-Azhar University, Cairo, Egypt ; Education College for Girls, Mosul University, Mosul, Iraq.
authors.forename: Mohammed W
authors.initials: MW
authors.lastname: Al-Neama
authors.affiliation: Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt.
authors.forename: Naglaa M
authors.initials: NM
authors.lastname: Reda
authors.affiliation: Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt.
authors.forename: Fayed F M
authors.initials: FF
authors.lastname: Ghaleb
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003205:Computing Methodologies; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software