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[Arabidopsis] announcement & request for feedback - Integrated Genome Browser for Arabidopsis data

Ann Loraine via arab-gen%40net.bio.net (by aloraine from gmail.com)
Thu May 3 21:40:31 EST 2007

Dear Arabidopsis researchers,

I am writing to announce a new free tool - PlantIGB - for visualization of
Arabidopsis genomic data - and hopefully other plant data soon.

You can download a copy and run it on your computer by visiting this link:


I would be grateful for any feedback you can give us - such as data sets
you'd like to see, advice on how to make the documentation clearer,
suggestions on ways to make the software easier to use, and ideas for new

This tool is mainly useful for in-depth analyses of large genomic regions,
or when you need to look carefully at a lot of genes in a short period of
time. For example, if you are doing a project involving analyses of many
different splice variants, this tool will likely be very useful. This tool
is also good for visualizing  genome-scale data sets, such as tiling array
or ChIP-chip data. To show you how this works, we've also posted some sample
tiling array data files you can experiment with, if you like -- see:

If you are a data provider, you can also set up a version of the tool on
your own Web site to disseminate your results. This aspect is not yet
well-documented - we're working on a set of instructions explaining how to
do it. (In a nutshell, you would use Java Web Start to distribute the
software, and you set up a "Quickload" Web directory to distribute your data
files.) Please contact me if you're interested in giving it a try -- because
if this turns out to be an in-demand feature, we can put more energy into
making it easier to do.


Ann Loraine

Ann Loraine
Assistant Professor
University of Alabama at Birmingham

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