I heard about RNAfold yesterday and started wondering if there were any other sites that could help predict the shape of your RNA sequence. From RNAfold’s site, I got links to other sites and eventually a bunch of programs and on-site servers that give insight about RNA’s interaction.
The following links are programs and sites I found that should hopefully help you analyze RNA sequence better. I’ve only had the chance to try a few of them:
The 1st one I tried was RNAshapes. It’s a small program that shows you the alternative shapes that you could get and their probabilities of occuring. There are a lot of data I don’t understand but I think someone should figure out all there is to know about the settings and data real soon.
I also loaded up donald 94 on Sfold, that seems to run from sFold and mFold’s engine and it gives you a lot different stats about your RNA and clean graphs for the visuals amongst us.
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RNA folding program:
UNAFOLD: http://mfold.rna.albany.edu/?q=DINAMe…
mFOLD: http://mfold.rna.albany.edu/?q=mfold/…
XRNA: http://rna.ucsc.edu/rnacenter/xrna/xr…
pKnot: http://bibiserv.techfak.uni-bielefeld…
RNAshapes: http://bibiserv.techfak.uni-bielefeld…
RNA On-site rendering:
Kinefold: http://kinefold.curie.fr/cgi-bin/form.pl
mFOLD: http://mfold.rna.albany.edu/?q=mfold/…
Genebee: http://www.genebee.msu.su/services/rn…
Sfold: http://sfold.wadsworth.org/cgi-bin/in…
VARNA: http://varna.lri.fr/demo.html
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If you’re not sure what program to try out, you could always get names from wikipedia and search them online!