Parallel performance evaluation of sequence nucleotide alignment on the supercomputer BlueGene/P

Authors:
Plamenka Borovska;Veska Gancheva;Stoyan Markov
Affiliations:
Computer Systems Department, Technical University of Sofia, Sofia, Bulgaria;Computer Systems Department, Technical University of Sofia, Sofia, Bulgaria;Computer Systems Department, Technical University of Sofia, Sofia, Bulgaria
Venue:
ECC'11 Proceedings of the 5th European conference on European computing conference
Year:
2011

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Abstract

Bioinformatics is a scientific area requiring powerful computing resources for exploring large sets of biological data. Sequence alignment is an important method in DNA and protein analysis. BLAST has become the most popular tool and implements a fast heuristic method for sequence alignment and searching. The goal of this paper is to estimate the scalability of parallel sequence alignment on the supercomputer BlueGene/P for the case study of investigating the interaction between influenza virus A and the host genome. Parallel performance evaluation of sequence alignment have been performed experimentally on the basis of parallel mpiBlast program implementation and conducted on a local mirror database comprising the available isolates of the influenza virus A and the human genome. The molecular biology outcome of the experiments is that the similarity of influenza virus A and human genome have been determined.