Click redraw to refresh the view to show/hide labels. Turn on/off labels for zoom view and genome view (press i button in bottom left corner).Click the chromosome again to return the whole genome view. Clicking on a chromosome will expand that chromosome and enlarge and label the features making them easier to view.Clicking on a feature can open up a new browser window with a cusomizable URL, eg a gene report page.Click again to turn each feature's highlight off. This can be used to turn on the region highlights for multiple features to better visualize their overlapping regions. Clicking on a feature toggles the highlight display so it will stay on when you move the mouse away.
Placing the mouse over individual features brings up a tooltip displaying the feature's name, it also visually highlights the region of the chromosome that the feature is aligned with.Features appear at the appropriate position on the chromosome and then dynamically move out to form a non-overlapping display.red/green/yellow for expression levels, peptide coverage or Xcorr for proteomic data. Annotations can be colored independently, allowing further information to be conveyed (eg. Annotations can come from a static XML file or can be dynamically generated by a server-side script.Bands can link out to a URL defined in the base map (to allow users to click to view a region in a genome browser, for example).This can also be used to portray any other custom backdrop for a chromosome - colored segments corresponding to syntenic regions in other organisms, colored according to feature density, etc. Perl scripts are available to take the UCSC cytogenetic map files and convert them to the appropriate XML format. Uses a base map containing the chromosomes and banding pattern of the desired organism.Here are some of the Flash GViewer's current features: It requires Macromedia Flash Plugin Version 7, you can download the plugin here. To make a more stand-alone solution I rewrote much of the functionality into a Flash application that is more adaptable to other organisms and other types of data. For our proteomics projects we were interested in viewing the genomic locations of the proteins identified in a proteomics experiment and a GViewer-like display is well suited to this. The Rat Genome Database has an SVG-based genome viewer that shows the location of genes and QTLs against a backdrop of the rat cytogenetic map. Simon Twigger, Medical College of Wisconsin © 2005 A customizable web tool for visualizing genome-wide annotation
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