V5 release - gene indicating function

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Saturday, June 2, 2012

Version 5 of Wash U Browser is available now. Follow this link and obtain the source code: http://epigenomegateway.wustl.edu/source/

New features

Sometimes the genes can only have parts but not the whole displayed in genome browser. For example when viewing a short interval centering over transcription start sites of genes in Gene Set View:

V5 release - gene indicating function 1 2.png

Genes in the gene track are partially displayed in above view. As a result it would be difficult for user to view the gene's entire structure unless he/she quits Gene Set View and relocates to this gene.

Now this problem is solved with the gene indication function. You only need to click on this gene to invoke the tooltip balloon and it will show you:

V5 release - gene indicating function 2 1.png

On the top of balloon, a small graph is drawn to display the gene in its entirety. As usual, the thin lines indicate introns, thick blocks are exons, and the smaller blocks at each end are untranslated regions (UTRs). A yellow box marks the part of the gene that's currently visible in the gene track.

Size of this graph is constant, it won't change with the actual length of the gene or balloon size. And the graph won't show up for genes completely displayed in the track. Currently there's no clickable function attached to this graph, but I wonder if user will find it useful to be able to control the plotting color by clicking it? Anything else?

Like I promised, the gene tooltip balloon is turning into a fully loaded dashboard. More interesting and useful functions will be added here to let you know, recognize, study, and operate the gene under your focus. Hang on with us!

Bug fixes

Imprecise gene placement in the gene track during gene set view is fixed Imprecise indicator (blue rectangle) placement over small chromosome ideogram on top left corner of the page is fixed.