How To Compare A Number Of Consensus Rna Secondar Structures.
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).
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Biostar
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mahesh.insilico •
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mahesh.insilico •
2 answers
you can also try Infernal: http://infernal.janelia.org/
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.
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