A parallel Euler approach for large-scale biological sequence assembly
Shi, Wei and Zhou, Wanlei 2005, A parallel Euler approach for large-scale biological sequence assembly, in Third International Conference on Information Technology and Applications : 4-7 July 2005, Sydney, Australia : proceedings, IEEE Computer Society, Los Alamitos, Calif., pp. 437-441.
Biological sequence assembly is an essential step for sequencing the genomes of organisms. Sequence assembly is very computing intensive especially for the large-scale sequence assembly. Parallel computing is an effective way to reduce the computing time and support the assembly for large amount of biological fragments. Euler sequence assembly algorithm is an innovative algorithm proposed recently. The advantage of this algorithm is that its computing complexity is polynomial and it provides a better solution to the notorious “repeat” problem. This paper introduces the parallelization of the Euler sequence assembly algorithm. All the Genome fragments generated by whole genome shotgun (WGS) will be assembled as a whole rather than dividing them into groups which may incurs errors due to the inaccurate group partition. The implemented system can be run on supercomputers, network of workstations or even network of PC computers. The experimental results have demonstrated the performance of our system.
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Field of Research
080699 Information Systems not elsewhere classified
Socio Economic Objective
970108 Expanding Knowledge in the Information and Computing Sciences
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