The Bluejay Genome Browser
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- Abstract
- Table of Contents
- Figures
- Literature Cited
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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PDF or HTML at Wiley Online LibraryTable 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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Figure 10.9.1 Bluejay download page showing three options available for using Bluejay: Application, Java Web Start, and Java Applet. They are recommended in the order shown, with the Applet option reserved for only quick and simple testing purposes, due to the restrictions on memory usage in Java applets. View Image -
Figure 10.9.2 Bluejay installer page showing available installers for widely used platforms as well as the recommended installer for the local platform (rectangular box at the center). If the local computer does not have Java installed, the installer version including Java VM (if available) can be downloaded and installed. View Image -
Figure 10.9.3 The Bluejay display just after successful loading of the Sulfolobus solfataricus P2 genome. There are three major viewing areas: the main drawing canvas (right), the context data tree pane (upper left), and the tab pane (lower left). The genome is displayed around a backbone (the thick yellow circle), with the tick marks representing the base pair positions and the rectangles along the backbone representing genomic elements (e.g., genes). The Context Tree shows the hierarchical genome data structure found in the input genome XML file. There are multiple tabs activated at any given time, and the tab pane shows the currently selected tab. By default, this is the Legend tab showing the assignment of colors to various genomic element categories. The user can perform actions on all these viewing areas, as well as the address bar (at the top), the zoom bar (below the address bar), and the search bar (bottom right). These actions change what is displayed and how the view is rendered. View Image -
Figure 10.9.4 Two successive graphical zoom operations applied on a genome display. From top to bottom, the selected region is shown in higher resolution, with more details of the gene annotation shown as appropriate zoom scales are reached, at which individual genes are shown. View Image -
Figure 10.9.5 Three ways to view reading frames in a genome. The default mode is Two Frame, which shows two lanes corresponding to positive and negative DNA strands (top). The Single Frame mode merges everything into one lane, but differentiates the DNA strands by the arrow directions (middle). The Six Frame mode shows all six possible reading frames separately in their own lanes (bottom). View Image -
Figure 10.9.6 A linear shape representation of a genome. This display was generated from the circular shape shown at the top of Figure by selecting Linear in the Shape tab, which was activated by selecting View–Show Shape Tab. View Image -
Figure 10.9.7 A bar chart showing the relative frequencies of functional categories present in a genome. This display was generated from the one in Figure by selecting View–Chart–Bar Chart. View Image -
Figure 10.9.8 Navigation using base pair positions. To move to a specific genomic region, click the Navigation tab, change the “at position” by entering a specific base pair number or moving the slider, and click Apply. View Image -
Figure 10.9.9 Navigation using text search. Searching for the term “kinase” results in 44 matches listed in the Search Results tab (top). Clicking on one of the items gives the user the option of creating a waypoint on that item, as shown by the Create Waypoint confirmation dialog and the panel. The genome display will change to set the focus on the selected genomic feature, with a waypoint flag attached to it (bottom). It is not necessary to create a waypoint to navigate to a searched position, but it makes it easier to return to the same position later or compare the same region from multiple genomes. View Image -
Figure 10.9.10 Navigation using waypoints. A second waypoint is created (top), the region around Waypoint2 is being zoomed in (second), the region around Waypoint2 is in focus, Waypoint1 is clicked to change the focus (third), and the region around Waypoint1 is in focus again (bottom). View Image -
Figure 10.9.11 Linking to external Web Services using the Seahawk Moby client. Left click on any gene to bring up a series of menus that can be followed until a list of menu items that says “Run … ” is reached (top). The requested service, querying the definition of the Gene Ontology term for the clicked gene in this example, will be run, and the response will be returned in a separate window (bottom). View Image -
Figure 10.9.12 Comparison and alignment of two genomes. A pair of linked genes (one from each genome) means that the two genes belong to the same category (top). The outer genome was rotated slightly to globally align the genes as much as possible (middle). Only those links with an angular distance less than 10% of the full circle are shown (bottom). View Image -
Figure 10.9.13 Loading gene expression data. Selecting Microarray–Open Project (top) brings up the Microarray Project Loader, where the directory containing the expression data files can be selected (middle). After the data files are loaded, a circle appears, along which the loaded expression values will be plotted (bottom). Note that the repeat regions were hidden for visual clarity (see above). View Image -
Figure 10.9.14 Expression ratio list. This is a table of gene IDs and expression ratios, sorted in descending order of the ratios. View Image -
Figure 10.9.15 Gene expression dataset ready to be played as an animation. The Experiments tab shows the information identifying the experiments and the current mode of viewing. In the Player Mode, the expression value bars will change in place as the player goes through different experiments. In this example, the experiments were performed as a time series over 11 time points, from 0 hr to 8.5 hr. View Image -
Figure 10.9.16 Gene cluster information window. The top part shows the expression line graphs for all the genes in the cluster, which collectively depicts the trend of expression value changes for this cluster. The bottom part is a color representation of expression values for each gene, where the values range from blue (lowest) to green (highest). View Image -
Figure 10.9.17 Generating a custom cluster. After text search, the genes in the search results are grouped together by creating a custom cluster. The Custom Cluster Generator allows the user to specify the source of the gene list, edit the list, and create the cluster. The newly created cluster can be viewed just like a cluster created by running a clustering algorithm on the whole genome. View Image
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Literature Cited
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| 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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