Chapter 13. Sequence Assembly and Finishing Methods

  1. Andreas D. Baxevanis3 and
  2. B. F. Francis Ouellette4
  1. Rodger Staden1,
  2. David P. Judge2 and
  3. James K. Bonfield1

Published Online: 11 JAN 2002

DOI: 10.1002/0471223921.ch13

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition

How to Cite

Staden, R., Judge, D. P. and Bonfield, J. K. (2001) Sequence Assembly and Finishing Methods, in Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Volume 43, Second Edition (eds A. D. Baxevanis and B. F. F. Ouellette), John Wiley & Sons, Inc., New York, USA. doi: 10.1002/0471223921.ch13

Editor Information

  1. 3

    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland

  2. 4

    Centre for Molecular Medicine and Therapeutics, Children's and Women's Health Centre of British Columbia, University of British Columbia Vancouver, British Columbia, Canada

Author Information

  1. 1

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom

  2. 2

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

Publication History

  1. Published Online: 11 JAN 2002
  2. Published Print: 20 APR 2001

ISBN Information

Print ISBN: 9780471383901

Online ISBN: 9780471223924

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Keywords:

  • sequence assembly;
  • finishing methods;
  • base cell accuracy;
  • confidence values;
  • assembly software;
  • global assembly;
  • file format;
  • readings;
  • Gap4;
  • Contig;
  • template display;
  • consistency display;
  • automation

Summary

This chapter presents a practical discussion of the two major methods used to assemble single-pass sequence data (< 500 bases) into complete, full-length contiguous sequence (Contigs). A problem set appears at the end of the chapter.