Doing RNA folding online for 1200 nt long sequence

Question

[caggtaagtat]

Hi,

I have a 1200 nt long RNA sequence and I would like to calculate the free energy for its structure, without downloading anything if possible.

Answer 1

[Joe]

There are many, many online webservers for this. Just google RNA folding webservers.

First result:

http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

[biofalconch]

"Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free energy"

Yeap, your sequence is not long enough to exceed the limits, go for it

[caggtaagtat]

Thanky you very much, I think my search missed the word "webserver".

Could you maybe also recommend a programm/package, to do the calculation automatically in R?

[Joe]

I’m afraid I personally don’t know of one (I’m not a heavy user of R for bioinformatics). There may be something in the bioconductor suite, you could start by looking for a vignette on their site perhaps,

Answer 2

[Eric Lim]

In addition to RNAfold,

Sfold: http://sfold.wadsworth.org/cgi-bin/index.pl

Mfold: http://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form