Question: Consensus secondary RNA stractures
0
gravatar for blur
2.3 years ago by
blur110
European Union
blur110 wrote:

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!

ADD COMMENTlink modified 2.3 years ago by jrj.healey12k • written 2.3 years ago by blur110

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

ADD REPLYlink written 2.3 years ago by agata88790
1
gravatar for jrj.healey
2.3 years ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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

ADD COMMENTlink written 2.3 years ago by jrj.healey12k
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