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A Parallel Programming Framework for Multi-core DNA Sequence Alignment

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2 Author(s)
Tiago José Barreiros Martins de Almeida ; INESC-ID, Tech. Univ. Lisbon, Lisbon, Portugal ; Nuno Filipe Valentim Roma

A new parallel programming framework for DNA sequence alignment in homogeneous multi-core processor architectures is proposed. Contrasting with traditional coarse-grained parallel approaches, that divide the considered database in several smaller subsets of complete sequences to be aligned with the query sequence, the presented methodology is based on a slicing procedure of both the query and the database sequence under consideration in several tiles/chunks that are concurrently processed by the several cores available in the multi-core processor. The obtained experimental results have proven that significant accelerations of traditional biological sequence alignment algorithms can be obtained, reaching a speedup that is linear with the number of available processing cores and very close to the theoretical maximum.

Published in:

Complex, Intelligent and Software Intensive Systems (CISIS), 2010 International Conference on

Date of Conference:

15-18 Feb. 2010