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A parallel DNA fragment assembly algorithm based on eulerian superpath approach

Zheng, Weimin, Shi, Wei and Zhou, Wanlei 2004, A parallel DNA fragment assembly algorithm based on eulerian superpath approach, Online journal of bioinformatics, vol. 5, pp. 91-101.

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Title A parallel DNA fragment assembly algorithm based on eulerian superpath approach
Author(s) Zheng, Weimin
Shi, Wei
Zhou, Wanlei
Journal name Online journal of bioinformatics
Volume number 5
Start page 91
End page 101
Publisher Pestsearch International
Place of publication Daisy Hill, Qld
Publication date 2004
ISSN 1443-2250
Keyword(s) DNA
fragment assembly
algorithm
eulerian
Summary Fragments assembly is among the core problems in the research of Genome. Although many assembly tools based on the "overlap-layout-consensus" paradigm are widely used such as in the Human Genome Project currently, they still can not resolve the "repeats problem" in the DNA sequencing. For the purpose of resolving such problem, Pevzner et al. put forward a new Euler Superpath assembly algorithm. But it needs a big and complex de Bruijin graph which consumes large amounts of memories i.e. becomes the bottleneck of the performance. We present a parallel DNA fragment assembly algorithm based on the Eularian Superpath theory and solve the bottleneck in the current assembly program. The experimental results demonstrate that our approach has a good scalability, and can be used in DNA assembly of middle and large size of eukaryote genome.
Notes Reproduced with the kind permission of the copyright owner.
Language eng
Field of Research 080301 Bioinformatics Software
HERDC Research category C1 Refereed article in a scholarly journal
Persistent URL http://hdl.handle.net/10536/DRO/DU:30008662

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