Question: Doing RNA folding online for 1200 nt long sequence
0
gravatar for caggtaagtat
16 months ago by
caggtaagtat500
caggtaagtat500 wrote:

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.

rna-folding rna • 523 views
ADD COMMENTlink modified 16 months ago by Eric Lim1.3k • written 16 months ago by caggtaagtat500
3
gravatar for jrj.healey
16 months ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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

ADD COMMENTlink written 16 months ago by jrj.healey12k

"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

ADD REPLYlink written 16 months ago by biofalconch390

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?

ADD REPLYlink written 16 months ago by caggtaagtat500

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,

ADD REPLYlink written 16 months ago by jrj.healey12k
0
gravatar for Eric Lim
16 months ago by
Eric Lim1.3k
Boston
Eric Lim1.3k wrote:

In addition to RNAfold,

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

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

ADD COMMENTlink modified 16 months ago • written 16 months ago by Eric Lim1.3k
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