A New DNA Fragment Assembly Method Based on Long Fragment Filtration

As an important aspect of bioinformatics, the main problem of Genome Sequencing is DNA Fragment Assembly. This paper proposed a new fragment assembly algorithm based on the long fragment filtration. Firstly, the fragment set was divided into two parts according to a threshold of the filtration lengt...

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Bibliographic Details
Main Authors: Quan, Guang-Ri, Xu, Yong-Dong, Wang, Ya-Dong, Xu, Zhi-Ming
Format: Conference Proceeding
Language:English
Subjects:
Assembly
Bioinformatics
Costs
DNA
DNA sequencing
Eulerian Super path
Filtration
Fragment assembly
Fragment filtration
Genomics
Heuristic algorithms
Partitioning algorithms
Sequences
Spatial resolution
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Summary:As an important aspect of bioinformatics, the main problem of Genome Sequencing is DNA Fragment Assembly. This paper proposed a new fragment assembly algorithm based on the long fragment filtration. Firstly, the fragment set was divided into two parts according to a threshold of the filtration length and the Bruijn graph was formed by the short fragments set. Subsequently system automatically selected long fragments which met the filtration condition by the Bruijn graph and the path searching method and constructed the filtrated fragments set. On the basis of not missing essential fragment information in the process of fragment assembly, our method effectively resolved the problem of high spatial cost and limited processing scale caused by traditional Eulerian Super path method. Finally, we certified the feasibility and the validity of our method through a series of experiments.
ISSN:1948-2914
1948-2922
DOI:10.1109/BMEI.2008.175