Consensus secondary RNA stractures

Question

[blur]

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!

[agata88]

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

Answer 1

[Joe]

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:

http://bioinfo.lifl.fr/RNA/gardenia/gardenia.php