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Old 02-03-2012, 06:27 AM   #1
Location: Pittsburgh, PA

Join Date: Feb 2011
Posts: 49
Lightbulb Viewing Mummer Aligments

Hey Guys!

I'm assuming that a lot of you out, like myself, use the bejesus out of mummer. If your PI is anything like mine, they prefer the results to be graphical, colorful, and aesthetically pleasing. If both of these criteria are true then you should check out the "coords-view" script that I wrote that views the output of 'show-coords -lcTH' as a pile-up sort of view. Here's the link to the Sourceforge page. Feedback is highly recommended and a citation if at all possible

It requires the Bioperl-graphics-2.25 and the intent is to allow all parameters of the Bioperl graphics modules to be implemented and fully customizable. This script still needs some work (which it is undergoing now) but it still produces nice images and is easy to use from the command line.

The interface follows that of the mummer software and I will stick to that. I'll also take suggestions and try to implement them as best I can. If you do use it, please provide feedback (good or bad), thank you very much!
twaddlac is offline   Reply With Quote

bioperl, mapping, mummer, perl

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