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  #1  
Old 23rd June 2013, 10:50 PM
GSft GSft is offline
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Join Date: May 2011
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Question An Offline chromosome browser that shows over lapping segments

Does anyone know of an offline chromosome browser that shows over lapping segments, similar to gedmatch, that would use raw data? If not, what programming language would be the easiest to do this with?

Does anyone use any of the programs/tools in these links?

http://home.earthlink.net/~odoniv/Ha...DNA_Tools.html

Thanks.
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Old 24th June 2013, 02:14 PM
Jomid59 Jomid59 is offline
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You can try this.
I have found it to be quite useful for comparing sequences.

http://www.mbio.ncsu.edu/BioEdit/bioedit.html
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Old 26th June 2013, 02:51 AM
GSft GSft is offline
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Thank you for the info
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Old 16th July 2013, 04:54 AM
K Son
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A quick and easy way to graph segments is with a spreadsheet and a stock chart. The start and stop points are used to draw the bar:
Here is a quick example done with LibreOffice:
http://i1297.photobucket.com/albums/...ps84befc15.jpg

The data used for the graph is in the upper left. The window at the bottom just shows the chart wizard with the stock chart selected. You have to change the line/bar width and color and rotate the chart to make it look better, but if you are familiar with spreadsheet charts that should be pretty simple.

If you want to do a multi-chromosome chart, it is possible to still use a spreadsheet and a staked chart but it is bit more complicated.
Here is an example of graph using a stacked chart:
http://i1297.photobucket.com/albums/...psedaa5acf.jpg
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