I was thinking of using OrthoMCL to cluster RNA sequences. Does anybody know whether it is OK? Thanks!
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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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Thanks so much!Originally posted by robinvvelzen View PostAs 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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