Chapter 12. Software for Restriction Fragment Physical Maps

  1. Prof. Dr. Khalid Meksem2,
  2. Prof. Dr. Günter Kahl3
  1. William Nelson,
  2. Carol Soderlund

Published Online: 28 APR 2005

DOI: 10.1002/3527603514.ch12

Book Title

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

The Handbook of Plant Genome Mapping: Genetic and Physical Mapping

Additional Information

How to Cite

Nelson, W. and Soderlund, C. (2005) Software for Restriction Fragment Physical Maps, in The Handbook of Plant Genome Mapping: Genetic and Physical Mapping (eds K. Meksem and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527603514.ch12

Editor Information

  1. 2

    Dept. Plant, Soil, Agriculture Southern Illinois University, Carbondale, IL 629, USA

  2. 3

    Plant Molecular Biology Biocentre and GenXPro Johann Wolfgang Goethe University Marie-Curie-Strasse 9 60439 Frankfurt am Main, Germany

Author Information

  1. Arizona Genome Computational Laboratory, Institute for Biomedical Science and Biotechnology, 303 Forbes Building, University of Arizona, Tucson, AZ 85721, USA

Publication History

  1. Published Online: 28 APR 2005
  2. Published Print: 26 JAN 2005

ISBN Information

Print ISBN: 9783527311163

Online ISBN: 9783527603510

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CHAPTER TOOLS

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Keywords:

  • plant genome mapping;
  • physical mapping;
  • software for restriction fragment physical maps;
  • review of agarose fingerprinting and FPC;
  • HICF techniques;
  • processing HICF data;
  • building HICF maps in FPC

Summary

This chapter contains sections titled:

  • Introduction

    • Review of Agarose Fingerprinting and FPC

  • HICF Techniques

    • Generalities

    • Approaches Using Type IIS Enzymes

    • SNaPshot HICF

  • Processing HICF Data

    • Peak Scoring

    • Sizing of Fragments

    • Quality and Contamination Screening

    • Vector and Repeat Screening

    • Packaging HICF Data for FPC

    • GenoProfiler

  • Building HICF Maps in FPC

    • Creating a New Project, Loading the Fingerprints, and Screening Vectors

    • Tolerance and Gel Length

    • Cutoff

    • Building

    • Build Quality, Q Clones, and the DQer

    • multiFPC

  • Theoretical Aspects

    • Simulations

    • Overlap Equations

  • Acknowledgments

  • References

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