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  • maimaiti2008
    Member
    • Apr 2013
    • 16

    #1

    Can OrthoMCL be used to cluster RNA sequences?

    I was thinking of using OrthoMCL to cluster RNA sequences. Does anybody know whether it is OK? Thanks!
  • robinvvelzen
    Junior Member
    • Jan 2013
    • 5

    #2
    As far as I know, orthoMCL uses a set of protein sequences as input. So orthoMCL will not work with RNA (cDNA) sequences directly (but would after translating them into protein sequences).
    In any case, homology/orthology assessment is much more powerful for protein sequences than for DNA sequences.

    Comment

    • maimaiti2008
      Member
      • Apr 2013
      • 16

      #3
      Originally posted by robinvvelzen View Post
      As far as I know, orthoMCL uses a set of protein sequences as input. So orthoMCL will not work with RNA (cDNA) sequences directly (but would after translating them into protein sequences).
      In any case, homology/orthology assessment is much more powerful for protein sequences than for DNA sequences.
      Thanks so much!

      Comment

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