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Bioinformatics Advance Access published online on February 24, 2006
Bioinformatics, 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
Received September 30, 2005
Revised February 2, 2006
Accepted February 19, 2006

Article

Refinement of optical map assemblies (original paper)

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

1 Department of Mathematics, University of Southern California
2 Department of Statistics, Harvard University
3 Laboratory for Molecular and Computational Genomics, Departments of Genetics and Chemistry, University of Wisconsin-Madison

* To whom correspondence should be addressed.
Anton Valouev, E-mail: valouev{at}usc.edu


  Abstract

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 nucleotides 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 bps. 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 (< 20x). We utilize a hidden Markov model to represent the consensus map and use the EM 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.

* These two authors contributed equally to this work.

Associate Editor: Keith A Crandall


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Home page
 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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