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  • 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!

  • #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.

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    • #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!

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