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Exon Visualization Tool (Early Beta)


All I see is a gray box!
What's being shown?
How do I control which sequences are displayed?
What does the options menu do?
Bugs/Known Issues/To-do
Where is the source code?
E-mail the author

All I see is a gray box!

Make sure you have the latest (at least 1.4) version of Java installed and set up to work with your browser. (Click
here to download.) Applets are by their nature finicky and can be disabled by security settings on your browser. In particular, Internet Explorer may block the applet from loading. If this happen, there may be a toolbar that comes across the top of your screen. By clicking, "Allow blocked content" on the yellow toolbar, the applet can run. Also, the program and data are around 750KB. Over a slow connection (or if Stanford's servers are feeling finicky), it may take a while to load the program over the web. If, for whatever reason, the program is not loading in your browser, you can always e-mail me (anthony.fodor@gmail.com) and I can send you a version that will run as a stand-alone application.

What's being shown?

This program displays the exon structure of the alpha subunit of the large-conductance calcium-activated (BK) K+ channel. Each BK channel sequence in mouse, rat, cow, human, chicken, drosophila and C. Elegans unigene clusters were mapped with BLAST to the Mouse, Human, Chicken and Drosophila genomes. Each row in the main viewing area represents a distinct Genbank sequence. Each point in the main viewing area is a region of homology between the Genbank sequence and the genomic sequence. The red lines at the top of the main viewing area represent the known transmembrane domains of the BK channel.

In order to catalog alternative splices of the BK channel, we chose one transcript as our reference sequence. The 28 exons in the reference sequence were mapped to each genome. The vertical lines in the main viewing area reflect the boundaries of these 28 reference exons. We define an alternative splice as a transcript that has a different exon structure from the reference sequence.

How do I control which sequences are displayed?

The right panel controls which sequences are displayed and gives information about selected exons and provides a link to Genbank. This screenshot shows the function of each section of the right panel:


What does the options menu do?

To access the options menu, right-click (or cntrl-click on a Mac):

Bugs/Known Issues/To-do

Where is the source code?

The Java source code will be released when the program is done. I still have lots of major refactoring to do on this code (see the bugs list above!) You can e-mail me (anthony.fodor@gmail.com) if for some reason you want the code before the refactoring is done. Also, comments, questions and further bug reports would all be appreciated.