GMOD

GBrowse syn PAG tutorial

This tutorial walks you through how to install and configure the GBrowse_syn comparative genomics viewer. This tutorial was originally taught by Sheldon McKay at the 2009 GMOD Schools - Europe & Americas. The notes and VMware image used on this page are from the Europe course.

Contents

• 1 VMware
• 2 Caveats
• 3 The Generic Synteny Browser
  • 3.1 Gbrowse_syn Introduction
  • 3.2 GBrowse_syn Documentation
  • 3.3 Whole Genome Alignments
• 4 Installing GBrowse_syn
• 5 Installing Gbrowse_syn
• 6 Configuration of GBrowse_syn
  • 6.1 Create a MySQL database
  • 6.2 Loading the alignment data
    • 6.2.1 The alignment data file
      • 6.2.1.1 Note on CLUSTALW
      • 6.2.1.2 Note on the sequence ID syntax
    • 6.2.2 The database loading script
      • 6.2.2.1 Running in the background with the linux screen command
  • 6.3 Setting up the species’ databases
    • 6.3.1 GFF3
    • 6.3.2 Loading
  • 6.4 Setting up the Configuration Files
  • 6.5 A Species Config File
  • 6.6 The GBrowse_syn Config File
  • 6.7 Testing the rice and wild_rice data sources in GBrowse
  • 6.8 Viewing the data in GBrowse_syn
• 7 Optional Advanced Section

VMware

This tutorial was taught using a VMware system image as a starting point. If you want to start with that same system, download and install the Starting image. See VMware for what software you need to use a VMware system image, and for directions on how to get the image setup and running on your machine.

Download Links will be added here

Caveats

Important Note

This tutorial describes the world as it existed on the day the tutorial was given. Please be aware that things like CPAN modules, Java libraries, and Linux packages change over time, and that the instructions in the tutorial will slowly drift over time. Newer versions of tutorials will be posted as they become available.

The Generic Synteny Browser

Optional Advanced Section

We will setup up a five-genome database if time permits.

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• Last updated at 18:53 on 8 October 2012.
• Content is available under a GNU Free Documentation License unless otherwise noted.