The Bluejay Genome Browser

Jung Soh1, Paul M.K. Gordon1, Christoph W. Sensen1

1 Visual Genomics Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 10.9
DOI:  10.1002/0471250953.bi1009s37
Online Posting Date:  March, 2012
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Abstract

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.

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

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Visualizing Genomes with Bluejay
  • Basic Protocol 2: Navigating Through Large Genomes
  • Basic Protocol 3: Linking to Biological Web Services
  • Basic Protocol 4: Comparing Multiple Whole Genomes or Genomic Regions
  • Basic Protocol 5: Visualizing Gene Expression Data
  • Basic Protocol 6: Producing High‐Quality Figures with Bluejay
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

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   Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, HS., Rios, D., Ritchie, G.R., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y.A., Trevanion, S., Vandrovcova, J., Vilella, A.J., White, S., Wilder, S.P., Zadissa, A., Zamora, J., Aken, B.L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández‐Suarez, X.M., Herrero, J., Hubbard, T.J., Parker, A., Proctor, G., Vogel, J., and Searle, S.M. 2011. Ensembl 2011. Nucleic Acids Res. 39:D800‐D806.
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   Fujita, P., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T.R., Giardine, B.M., Harte, R.A., Hillman‐Jackson, J., Hsu, F., Kirkup, V., Kuhn, R.M., Learned, K., Li, C.H., Meyer, L.R., Pohl, A., Raney, B.J., Rosenbloom, K.R., Smith, K.E., Haussler, D., and Kent, W.J. 2011. The UCSC Genome Browser database: Update 2011. Nucleic Acids Res. 39:D876‐D882.
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   Soh, J., Gordon, P.M.K., Taschuk, M.L., Dong, A., Ah‐Seng, A.C., Turinsky, A.L., and Sensen, C.W. 2008. Bluejay 1.0: Genome browsing and comparison with rich customization provision and dynamic resource linking. BMC Bioinformatics 9:450.
   Turinsky, A.L., Ah‐Seng, A.C., Gordon, P.M., Stromer, J.N., Taschuk, M.L., Xu, E.W., and Sensen, C.W. 2005a. Bioinformatics visualization and integration with open standards: The Bluejay genomic browser. In Silico Biol. 5:187‐198.
   Turinsky, A.L., Gordon, P.M., Xu, E.W., Stromer, J.N., and Sensen, C.W. 2005b. Genomic data representation through images: The MAGPIE/Bluejay system. In Handbook of Genome Research (C.W. Sensen, ed.) pp. 187‐198. Wiley‐VCH, Weinheim, Germany.
Internet Resources
  http://bluejay.ucalgary.ca/publications.html
  A list of all articles on Bluejay published so far, including online links to access them.
  http://www.geneontology.org/
  The Gene Ontology (GO) Web site, where the user can search for genes, proteins, or GO terms using the AmiGO GO Browser.
  http://www.w3.org/Graphics/SVG/
  The main portal for the Scalable Vector Graphics (SVG) format, including the SVG 1.1 specification and information on current developments.
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