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Comparing Assemblies Using Fragments and Mate-Pairs

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Algorithms in Bioinformatics (WABI 2001)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2149))

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Abstract

Using current technology, large consecutive stretches of DNA (such as whole chromosomes) are usually assembled from short fragments obtained by shotgun sequencing, or from fragments and mate-pairs, if a “double-barreled” shotgun strategy is employed. The positioning of the fragments (and mate-pairs, if available) in an assembled sequence can be used to evaluate the quality of the assembly and also to compare two different assemblies of the same chromosome, even if they are obtained from two different sequencing projects. This paper describes some simple and fast methods of this type that were developed to evaluate and compare different assemblies of the human genome. Additional applications are in “feature-tracking” from one version of an assembly to the next, comparisons of different chromosomes within the same genome and comparisons between similar chromosomes from different species.

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References

  1. A. Edwards and C.T. Caskey. Closure strategies for random DNA sequencing. METHODS: A Companion to Methods in Enzymology, 3(1):41–47, 1991.

    Article  Google Scholar 

  2. D. Haussler. Human Genome Project Working Draft. http://genome.cse.ucsc.edu.

  3. G. Jacobson and K.-P. Vo. Heaviest increasing/common subsequence problems. In Proceedings 3rd Annual Symposium on Combinatorial pattern matching (CPM), pages 52–66, 1992.

    Google Scholar 

  4. E. W. Myers, G. G. Sutton, A. L. Delcher, I. M. Dew, D. P. Fasulo, M. J. Flanigan, S. A. Kravitz, C. M. Mobarry, K. H. J. Reinert, K. A. Remington, E. L. Anson, R. A. Bolanos, H-H. Chou, C. M. Jordan, A. L. Halpern, S. Lonardi, E. M. Beasley, R. C. Brandon, L. Chen, P. J. Dunn, Z. Lai, Y. Liang, D. R. Nusskern, M. Zhan, Q. Zhang, X. Zheng, G. M. Rubin, M. D. Adams, and J. C. Venter. A whole-genome assembly of Drosophila. Science, 287:2196–2204, 2000.

    Article  Google Scholar 

  5. F. Sanger, A. R. Coulson, G. F. Hong, D. F. Hill, and G. B. Petersen. Nucleotide sequence of bacteriophage λ DNA. J. Mol. Bio., 162(4):729–73, 1992.

    Article  Google Scholar 

  6. F. Sanger, S. Nicklen, and A. R. Coulson. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74(12):5463–5467, 1977.

    Article  Google Scholar 

  7. J. C. Venter, M. D. Adams, E. W. Myers, et al. The sequence of the human genome. Science, 291:1145–1434, 2001.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Informatics Research, Celera Genomics Corp., 45 W Gude Drive, Rockville, MD, 20850, USA

    Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert & Granger G. Sutton

Authors
  1. Daniel H. Huson
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  2. Aaron L. Halpern
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  3. Zhongwu Lai
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  4. Eugene W. Myers
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  5. Knut Reinert
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  6. Granger G. Sutton
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Editor information

Editors and Affiliations

  1. LIRMM, 161 rue Ada, 34392, Montpellier, France

    Olivier Gascuel

  2. Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA

    Bernard M. E. Moret

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© 2001 Springer-Verlag Berlin Heidelberg

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Huson, D.H., Halpern, A.L., Lai, Z., Myers, E.W., Reinert, K., Sutton, G.G. (2001). Comparing Assemblies Using Fragments and Mate-Pairs. In: Gascuel, O., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2001. Lecture Notes in Computer Science, vol 2149. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44696-6_23

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  • DOI: https://doi.org/10.1007/3-540-44696-6_23

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42516-8

  • Online ISBN: 978-3-540-44696-5

  • eBook Packages: Springer Book Archive

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