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A parallel Euler approach for large-scale biological sequence assembly

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conference contribution
posted on 2005-01-01, 00:00 authored by W Shi, Wanlei Zhou
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.

History

Event

International Conference on Information Technology and Applications (3rd : 2005 : Sydney, Australia)

Pagination

437 - 441

Publisher

IEEE Computer Society

Location

Sydney, Australia

Place of publication

Los Alamitos, Calif.

Start date

2005-07-04

End date

2005-07-07

ISBN-13

9780769523163

ISBN-10

0769523161

Language

eng

Notes

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Publication classification

E1 Full written paper - refereed

Copyright notice

2005, IEEE

Editor/Contributor(s)

X He, T Hintz, M Piccardi, Q Wu, M Huang, D Tien

Title of proceedings

Third International Conference on Information Technology and Applications : 4-7 July 2005, Sydney, Australia : proceedings