Navigating Public Physical Mapping Databases

Lincoln D. Stein1

1 Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 5.16
DOI:  10.1002/0471142905.hg0516s13
Online Posting Date:  May, 2001
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This unit provides concise overviews of the many physical mapping resources available and relates them to the genetic and transcript maps. Useful information on resolution of the maps, how to access them, and how to interpret them is compiled and presented in a clear fashion. Especially useful is a set of detailed protocols describing how to construct an STS marker and how to map it by means of available yeast artificial chromosomes (YACs). An additional protocol describes accessing EST marker maps.

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Table of Contents

  • Types of Physical Maps
  • Genome‐Wide Maps from Large Community Databases
  • Basic Protocol 1: Navigating Chromosome Maps in NCBI Entrez
  • Basic Protocol 2: Navigating Chromosome Maps in GDB
  • Genome‐Wide Maps from Individual Sources
  • Basic Protocol 3: Browsing the NCBI Transcript Map
  • Basic Protocol 4: Creating an STS for Placement on the Whitehead Maps
  • Basic Protocol 5: Mapping an STS Relative to the Whitehead STS/YAC Content Map
  • Basic Protocol 6: Retrieving YAC Overlap from the CEPH Server
  • Chromosome‐Specific Maps
  • Figures
  • Tables
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Literature Cited

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Internet Resources
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  Full text of WWW Entrez: A hypertext retrieval tool for molecular biology. J.A. Epstein, J.A. Kans, and G.D. Schuler; Second International World Wide Web Conference Chicago, Illinois, 1994.
  Code available for Primer 3, S. Rozen. and H.J. Skaletsky, (1996)/.
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