Generic Genome Browser (GBrowse)

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Generic Genome Browser (GBrowse)

• Sravanthi Joginipelli

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Introduction

• GBrowse is a genome viewer
• Developed by GMOD
• Popular component of GMOD
• GMOD (Generic Model Organism Database project)
• Combination of database and interactive web page
• Manipulating and displaying annotations on genome
• see more and more personal genomes becoming
  available
• Price of sequencing genomes continues to drops
• good choice for a wide range of genome-viewing
  applications.

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Genome Databses

• MGI
• Flybase
• Dictybase
• International Hap Map Project
• Wormbase
• Human genome segmental duplication databse
• Xenbase
• Ecoli
• James Watsons Personal Genome Sequence
• Craig Venters personal Genome Sequence

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Software and Installation

• Free software
• Goal simplify standardize MODs
• Versions
• GBrowse 1.X
• GBrowse 2.0
• Perl 5.8.6 or higher and the Apache web server
• JBrowse
• Genome Browser
• Official successor of Gbrowse
• AJAX based interface

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• Lincoln D.Stein and his collegues

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• Universal and yet customizable web display
• Overall appearance looks similar to each model
  organism database
• Basic features of navigation, display and control
  similar
• Integration
• Specific annotations and plug-ins

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Browsing a Genome
birds eye view...
...or zoom in for details
customize it
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Excercise

• Use the Mouse Genome Browser (MGI) at
• http//gbrowse.informatics.jax.org/cgi-bin/gbrowse
  /
• Search for the mouse gene Ift88. To which
  chromosome and region does Ift88
• map? How many targeted alleles of Ift88 currently
  exist? What are some of the
• phenotypes associated with IIft88? Edit your
  Track options so that only
• cardiovascular phenotypes are displayed. At a 5
  Mbp view, how many other genes
• mapping near Ift88 also have a cardiovascular
  system phenotype?

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References

• GBrowse wikipedia
• http//gmod.org/wiki/Gbrowse
• OpenHelix, LLC. Tutorial on GBrowse
  http//www.openhelix.com/gbrowse
• GBrowse installation http//gmod.org/wiki/Gbrowse
  Installation

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• Thank you