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| Keywords | |
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genome sequencing |
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new generation sequencing |
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read mapping |
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optical mapping |
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sequence assembly |
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Eulerian graphs |
| Authors | |
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David C. Schwartz |
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Michael S. Waterman |
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
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.
This work is supported by NIH under Grant No. R01 HG000225 (DCS) and NSF of USA under Grant No. DBI-0501818 (DCS).
David C. Schwartz has been a professor of chemistry, genetics, and biotechnology at the University of Wisconsin-Madison since 1999. Previous faculty appointments were at New York University and The Carnegie Institution of Washington-Baltimore. He works at the interface between nanotechnology and genomic science through his invention of single molecule platforms for genome analysis. As a graduate student, he invented Pulsed Field Gel Electrophoresis and continues to train students in the science of how to conceive and develop new tools for biological investigation as the director of a training program.
Michael S. Waterman is university professor at the University of Southern California where he has been a faculty member since 1982. Prior to that he held positions at Los Alamos National Laboratory and Idaho State University. He also currently holds a chair professor team at Tsinghua University. Professor Waterman works in the area of computational biology, particularly on the analysis DNA, RNA and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a member of the U.S. National Academy of Sciences and of the French Académie des Sciences.