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5.6 years ago
jaqx008
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110
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
RNAalifold maybe (Vienna Package)
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?
https://www.tbi.univie.ac.at/RNA/RNAalifold.1.html :)
RNAalifold seem to be working. Thank you.
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?
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.
Ok. where can I get tRNA sequences from please?
Try http://rfam.xfam.org.