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Bioinformatics Advance Access originally published online on February 24, 2006
Bioinformatics 2006 22(10):1217-1224; doi:10.1093/bioinformatics/btl063
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Refinement of optical map assemblies

Anton Valouev 1,2,*,{dagger}, Yu Zhang 3,{dagger}, David C. Schwartz 4 and Michael S. Waterman 2

1 MCB 1050 Childs Way, Los Angeles, CA 90089-2910, USA
2 Department of Mathematics, University of Southern California Los Angeles, CA, USA
3 Department of Statistics, Harvard University MA, USA
4 Laboratory for Molecular and Computational Genomics, Departments of Genetics and Chemistry, University of Wisconsin-Madison WI, USA

*To whom correspondence should be addressed.

Motivation: Genomic mutations and variations provide insightful information about the functionality of sequence elements and their association with human diseases. Traditionally, variations are identified through analysis of short DNA sequences, usually shorter than 1000 bp per fragment. Optical maps provide both faster and more cost-efficient means for detecting such differences, because a single map can span over 1 million bp. Optical maps are assembled to cover the whole genome, and the accuracy of assembly is critical.

Results: We present a computationally efficient model-based method for improving quality of such assemblies. Our method provides very high accuracy even with moderate coverage (<20 x). We utilize a hidden Markov model to represent the consensus map and use the expectation-Maximization algorithm to drive the refinement process. We also provide quality scores to assess the quality of the finished map.

Availability: Code is available from www.cmb.usc.edu/people/valouev/

Contact: valouev{at}usc.edu

Received on September 30, 2005; revised on February 2, 2006; accepted on February 19, 2006

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 Proc. Natl. Acad. Sci. USAHome page
A. Valouev, D. C. Schwartz, S. Zhou, and M. S. Waterman
An algorithm for assembly of ordered restriction maps from single DNA molecules
PNAS, October 24, 2006; 103(43): 15770 - 15775.
[Abstract] [Full Text] [PDF]


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