Question: How do I predict consensus RNA structures?
0
gravatar for jaqx008
10 months ago by
jaqx00850
jaqx00850 wrote:

Hello all, I am trying to generate consensus RNA structures from a fasta output. I was going to use RNAforester to do it on the command line. I installed the RNAforester (the help menu shows up so I know I have it) but the usage is not giving me any output. I dont know if Im using it in the right way. is there any other known tool or way to do this? what program/tool works well, and or how do I make this command work to get the structures? Thanks

RNAforester -p -m in.fasta > out.fasta
mapping rna rnaforester • 359 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by jaqx00850
1

RNAalifold maybe (Vienna Package)

ADD REPLYlink written 10 months ago by cschu1811.7k

I did see Vienna package and installed it. but have no idea how the usage is. I looked but didnt find the usage. Do you know it?

ADD REPLYlink written 10 months ago by jaqx00850

https://www.tbi.univie.ac.at/RNA/RNAalifold.1.html :)

ADD REPLYlink written 10 months ago by cschu1811.7k

RNAalifold seem to be working. Thank you.

ADD REPLYlink written 10 months ago by jaqx00850

So I used the vienna package and the structure I am getting doesnt represent all my sequences in my alignment file. its just a big circle with one sequence patched to one side of the circle. am I missing something?

ADD REPLYlink written 10 months ago by jaqx00850

Maybe that is the consensus, in which case the structures of your RNAs are not very similar. I haven't worked in RNA structure for quite a while, so I might be missing something. To validate you could take a handful of tRNA sequences and see how the output looks like for those.

ADD REPLYlink written 10 months ago by cschu1811.7k

Ok. where can I get tRNA sequences from please?

ADD REPLYlink written 10 months ago by jaqx00850

Try http://rfam.xfam.org.

ADD REPLYlink written 10 months ago by cschu1811.7k
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