Using the NCBI Map Viewer to Browse Genomic Sequence Data

Tyra G. Wolfsberg1

1 Bethesda, Maryland
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 18.5
DOI:  10.1002/0471142905.hg1805s69
Online Posting Date:  April, 2011
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Abstract

This unit includes a basic protocol with an introduction to the Map Viewer, describing how to perform a simple text‐based search of genome annotations to view the genomic context of a gene, navigate along a chromosome, zoom in and out, and change the displayed maps to hide and show information. It also describes some of NCBI's sequence‐analysis tools, which are provided as links from the Map Viewer. The alternate protocols describe different ways to query the genome sequence, and also illustrate additional features of the Map Viewer. Alternate Protocol 1 shows how to perform and interpret the results of a BLAST search against the human genome. Alternate Protocol 2 demonstrates how to retrieve a list of all genes between two STS markers. Finally, Alternate Protocol 3 shows how to find all annotated members of a gene family. Curr. Protoc. Hum. Genet. 69:18.5.1‐18.5.25 © 2011 by John Wiley & Sons, Inc.

Keywords: genome browser; genome assembly; genomic sequence; gene map

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: General Navigation in the NCBI Map Viewer
  • Alternate Protocol 1: BLAST Search Against the Genome
  • Alternate Protocol 2: Using the NCBI Map Viewer to View a Region Between Two Markers
  • Alternate Protocol 3: Using the NCBI Map Viewer to Identify All Members of a Gene Family in the Mouse Genome
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: General Navigation in the NCBI Map Viewer

  Materials
  • Computer with Internet access
  • An up‐to‐date Internet browser, such as Firefox (Windows, Mac OS X, and Linux; http://www.mozilla.org/firefox); Safari (Windows, Mac OS X; http://www.apple.com/safari); or Internet Explorer (Windows; http://www.microsoft.com/ie)

Alternate Protocol 1: BLAST Search Against the Genome

  Materials
  • Computer with Internet access
  • An up‐to‐date Internet browser, such as Firefox (Windows, Mac OS X, and Linux; http://www.mozilla.org/firefox); Safari (Windows, Mac OS X; http://www.apple.com/safari); or Internet Explorer (Windows; http://www.microsoft.com/ie)

Alternate Protocol 2: Using the NCBI Map Viewer to View a Region Between Two Markers

  Materials
  • Computer with Internet access
  • An up‐to‐date Internet browser, such as Firefox (Windows, Mac OS X, and Linux; http://www.mozilla.org/firefox); Safari (Windows, Mac OS X; http://www.apple.com/safari); or Internet Explorer (Windows; http://www.microsoft.com/ie)

Alternate Protocol 3: Using the NCBI Map Viewer to Identify All Members of a Gene Family in the Mouse Genome

  Materials
  • Computer with Internet access
  • An up‐to‐date Internet browser, such as Firefox (Windows, Mac OS X, and Linux; http://www.mozilla.org/firefox); Safari (Windows, Mac OS X; http://www.apple.com/safari); or Internet Explorer (Windows; http://www.microsoft.com/ie)
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Figures

Videos

Literature Cited

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