UNIT 10.9 The Bluejay Genome Browser

  1. Jung Soh,
  2. Paul M.K. Gordon,
  3. Christoph W. Sensen

Published Online: 1 MAR 2012

DOI: 10.1002/0471250953.bi1009s37

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Soh, J., Gordon, P. M. and Sensen, C. W. 2012. The Bluejay Genome Browser. Current Protocols in Bioinformatics. 37:10.9:10.9.1–10.9.23.

Author Information

  1. Visual Genomics Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada

Publication History

  1. Published Online: 1 MAR 2012
  2. Published Print: MAR 2012


The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca. Curr. Protoc. Bioinform. 37:10.9.1-10.9.23. © 2012 by John Wiley & Sons, Inc.


  • genome browser;
  • comparative genomics;
  • genome annotation;
  • gene expression;
  • Gene Ontology;
  • Bluejay;
  • bioinformatics;
  • genomic data visualization