Consensus secondary RNA stractures
Hi,
I have a few thousands of secondary structures of RNA from RNAfold, and I'd love to find a consensus secondary structure. I saw RNAalifold - is it a good tool for what I want to do? also, can it handle these many sequences? Does anyone have other tools they recommend? Thanks!
1 answer
I'm not 100% certain that this tool can give you back the consensus as a file, but some people around our lab have been using it so might be worth checking out if you have (/can get) your trees in bracket notation:
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Do you has it as sequences? If so, you can perform aligment (ClustalO) and then use one form this post:
How To Obtain The Consensus Sequence From A Clustalo Result.
Best,
Agata