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  • Mehmet Göktay
    Junior Member
    • Sep 2014
    • 8
    #1

    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
    Tags: None
    • tymek666
      Junior Member
      • May 2011
      • 7
      #2
      There's several tools, I usually use msatcommander.

        Comment

        • Mehmet Göktay
          Junior Member
          • Sep 2014
          • 8
          #3
          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?

            Comment

            • tymek666
              Junior Member
              • May 2011
              • 7
              #4
              It depends on which machine I'm working
              Generally I used to run it under win7.

                Comment

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