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A parallel DNA fragment assembly algorithm based on eulerian superpath approach

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journal contribution
posted on 2004-01-01, 00:00 authored by W Zheng, W Shi, Wanlei Zhou
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.

History

Journal

Online journal of bioinformatics

Volume

5

Pagination

91 - 101

Publisher

Pestsearch International

Location

Daisy Hill, Qld

ISSN

1443-2250

Language

eng

Notes

Reproduced with the kind permission of the copyright owner.

Publication classification

C1 Refereed article in a scholarly journal

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