How To Compare A Number Of Consensus Rna Secondar Structures.

Question

[mahesh.insilico]

I have consensus RNA secondary structure of a number of groups belonging to a single species. how can i establish relation among them based on conservation annotation. I am using the Freiburg RNA tool (LocARNA).

Answer 1

[JC]

you can also try Infernal: http://infernal.janelia.org/

Answer 2

[Bioslayer]

Doesn't the locARNA output have a tree file that is viewable in njplot ??

Other than that, I guess using RNAclust.pl will get you to cluster these groups too as it interfaces locARNA for the sole purpose of clustering.

I am grappling with locARNA and RNAclust.pl myself at the moment as I get memory errors and all that for MSA..So we can share some of our experiences.