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GBrowse User Introductory Tutorial

Tutorial and training materials by OpenHelix

Learn to use GBrowse, a web application that allows you to explore genomic sequences together with annotated data. GBrowse is rapidly becoming a genomic browser of choice among organism databases, because the browser is both universal and yet customizable. Once you learn to use GBrowse at one database, you'll be able to use it to view any genome. Results can be customized to show only the data you want to see. The tool is flexible to allow you to upload and incorporate your own unpublished data into the genomic viewer. You'll have fun as you explore a variety of genomes (from paramecia to personal genomics) with the new perspective and detailed annotations that GBrowse provides.
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You'll learn:

  • the basic layout and search methods at GBrowse
  • how to access detailed annotation data tied to genomic sequences
  • how to select and customize annotations using Tracks
  • how to upload and incorporate your own data or other external data sources
  • take a tour of different GBrowse installations at model organism databases


Related tutorials

This tutorial is a part of the tutorial group Genome Browsers. You might find the other tutorials in the group interesting:


This tutorial is a part of the tutorial group Gramene-associated resources. You might find the other tutorials in the group interesting:

  • Gramene: A resource on rice and other grass genomes
  • BioMart: Management and querying of many types of biological data

Categories

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Recent BioMed Central research articles citing this resource

Reid Ian et al., SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models Sequence analysis (methods). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-229

Yang Hsin-Chou et al., Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-319

Zhang Yufan et al., The Theobroma cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation Reproductive biology. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-106

Hill-Burns M Erin et al., Identification of a novel Parkinson’s disease locus via stratified genome-wide association study Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-118

O’Bleness Majesta et al., Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-387

More about the resource:

GBrowse stands for “Generic Genome Browser”. It is a web application to view and explore annotated genomes. It was developed by GMOD, the Generic Model Organism Database, which is a community of biologists and computer programmers dedicated to the idea of making free, open-source software available to all model organism databases, or MODs, with the goal of simplifying and standardizing the appearance and usage of these MODs. When new genomes from different organisms are sequenced and a dedicated annotated database is created to serve that genome, the curators can use GBrowse to get their MOD up and running in no time.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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