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Online Journal of Bioinformatics

Volume 5:91-101, 2004.

A parallel DNA fragment assembly algorithm based on eulerian superpath.


Zheng W1, Shi W2*, Zhou W2


1Institute of High Performance Computing, Department of Computer Science and Technology, Tsinghua University, China. 2 School of Information Technology, Deakin University, Australia.




Zheng W, Shi W, Zhou W A, Parallel DNA Fragment Assembly Algorithm Based On Eulerian Superpath, Onl J Bioinform., 5:  91-101, 2004. Assembly tools based on overlap-layout-consensus paradigm do not resolve the problem of repeats in DNA sequencing. A parallel DNA fragment assembly algorithm based on the Eulerian Superpath which does not require (the memory laden) De-Bruijin graph, is described. The method proposes to resolve the bottlenecks in current assembly programs. The results demonstrate that the method has good scalability for DNA assembly of medium to large eukaryote genomes.


KEY-WORDS: DNA, Fragment Assembly, Algorithm, Eulerian