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Journal of Computer Science and Technology 2010, Vol. 25 Issue (1) :3-9    DOI:
Special Issue on Computational Challenges from Modern Molecular Biology Current Issue | Archive | Adv Search << Previous Articles | Next Articles >>
New Generations: Sequencing Machines and Their Computational Challenges
David C. Schwartz1 and Michael S. Waterman2,3
1Laboratory for Molecular and Computational Genomics, Department of Chemistry and Laboratory of Genetics, University of Wisconsin-Madison, WI 53706, U.S.A.
2Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, U.S.A.
3Department of Automation, Tsinghua University, Beijing 100084, China

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New generation sequencing systems are changing how molecular biology is practiced. The widely promoted $1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these developments and demands.

Articles by authors
David C. Schwartz
Michael S. Waterman
Keywordsgenome sequencing    new generation sequencing    read mapping    optical mapping    sequence assembly    Eulerian graphs     
Received 2009-09-05;

This work is supported by NIH under Grant No. R01 HG000225 (DCS) and NSF of USA under Grant No. DBI-0501818 (DCS).

Cite this article:   
David C. Schwartz and Michael S. Waterman.New Generations: Sequencing Machines and Their Computational Challenges[J]  Journal of Computer Science and Technology, 2010,V25(1): 3-9
Copyright 2010 by Journal of Computer Science and Technology