Parallel performance evaluation of multithreaded local sequence alignment

Authors:
Plamenka Borovska;Veska Gancheva;Galin Dimitrov;Krasimir Chintov
Affiliations:
Technical University of Sofia;Technical University of Sofia;Technical University of Sofia;Technical University of Sofia
Venue:
Proceedings of the 12th International Conference on Computer Systems and Technologies
Year:
2011

Citing 6
Cited 0

Fundamentals of Computer Alori

Fundamentals of Computer Alori
A Parallel Smith-Waterman Algorithm Based on Divide and Conquer

ICA3PP '02 Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing
Parallel Strategies for Local Biological Sequence Alignment in a Cluster of Workstations

IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 15 - Volume 16
Parallel Computing for Bioinformatics and Computational Biology (Wiley Series on Parallel and Distributed Computing)

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Striped Smith--Waterman speeds database searches six times over other SIMD implementations

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An exact parallel algorithm to compare very long biological sequences in clusters of workstations

Cluster Computing

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Abstract

Bioniformatics is area, demanding knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This scientific area requires powerful computing resources for exploring large sets of biological data. Biological sequence processing is a key for molecular biology. Smith-Waterman algorithm, based on dynamic programming has become the most fundamental in bioinformatics. The goal of this paper is to investigate the efficiency of parallel multithreaded implementation based on Smith-Waterman algorithm. Performance parameters have been estimated by the experiments using various data sets on two parallel computer platforms.