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Old 01-26-2015, 12:05 AM   #1
Mehmet Göktay
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Location: Izmir Turkey

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Lightbulb Finding SSRs on contigs

Hi everyone,

I need to search simpe sequence repeats(SSRs) on a de-novo assembled contigs. I aim to find perfect and almost perfect repeats on the contigs. Is there anyone who has experience with finding ssrs? If so, please give me an advice which tool should I use?

Best Regars,
Mehmet
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Old 01-26-2015, 12:14 AM   #2
tymek666
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There's several tools, I usually use msatcommander.
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Old 01-26-2015, 01:25 AM   #3
Mehmet Göktay
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Hi,
I tried to use msatcommander 0.8.2 version on linux. It worked but I suppose there is a newer version 1.0.2 but which doesn't work on linux. Which version do you use?
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Old 01-26-2015, 01:41 AM   #4
tymek666
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It depends on which machine I'm working
Generally I used to run it under win7.
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