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 The tool is flexible to allow you to upload and incorporate your own unpublished data into the genomic viewer.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.|
- 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
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:
Recent BioMed Central research articles citing this resource
Sharpe G Andrew et al., Ancient orphan crop joins modern era: gene-based SNP discovery and mapping in lentil Plant genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-192
Shen Shih Pei et al., Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins Neural development. BMC Developmental Biology (2013) doi:10.1186/1471-213X-13-1
Pavlopoulos A Georgios et al., Unraveling genomic variation from next generation sequencing data. BioData Mining (2013) doi:10.1186/1756-0381-6-13
Pirona Raul et al., Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach Genetics and crop biotechnology. BMC Plant Biology (2013) doi:10.1186/1471-2229-13-166
Zimmer D Andreas et al., Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions Plant genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-498
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.
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.