By Topic

Hybrid MPI/OpenMP Strategy for Biological Multiple Sequence Alignment with DIALIGN-TX in Heterogeneous Multicore Clusters

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

4 Author(s)
de Araujo Macedo, E. ; Dept. of Comput. Sci., Univ. of Brasilia (UnB), Brasilia, Brazil ; Magalhaes Alves de Melo, A.C. ; Pfitscher, G.H. ; Boukerche, A.

Multiple Sequence Alignment (MSA) is a fundamental problem in Bioinformatics that aims to align more than two biological sequences in order to emphasize similarity regions. This problem is known to be NP-Complete, so heuristic methods are used to solve it. DIALIGN-TX is an iterative heuristic method for MSA that is based on dynamic programming and generates alignments by concatenating ungapped regions with high similarity. This paper proposes an MPI/OpenMP master/slave parallel strategy to run DIALIGN-TX in heterogeneous multicore clusters, with multiple allocation policies. The results obtained in a 28-core heterogeneous cluster with real sequence sets show that the execution time can be drastically reduced. Also, we show that an appropriate choice of the allocation policy and the master node has great impact on the overall system performance.

Published in:

Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium on

Date of Conference:

16-20 May 2011