State-Of-The-Art Of Rna Structure Prediction Algorithms

Question

[tomas.iesmantas]

Hi

I'm looking for a paper that would review most important classes of algorithms for RNA secondary structure prediction. I googled quite a lot, but decided that it would be more faster and fruitful to ask people that have already extensive experience in the field. I am interested in the state-of-the-art review of available approaches/algorithms for RNA/DNA secondary structure prediction. Suggestions and links to the comprehensive papers will be greeted very much.

p.s. Tertiary structure prediction is of interest as well.

Answer 1

[Charles Warden]

Mfold is probably the most popular tool for RNA secondary structure prediction:

http://mfold.rna.albany.edu/?q=mfold

The developer of Mfold actually says that UNAFold is better (http://www.bioinfo.rpi.edu/applications/), but I find Mfold to be easier to use (and it is still the most popular choice).

RNAfold is another popular program: http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

Although not commonly used, there are also programs to predict RNA secondary structure based upon evolutionary conservation:

EvoFold: http://users.soe.ucsc.edu/~jsp/EvoFold/

RNAz: http://www.tbi.univie.ac.at/~wash/RNAz/

Strictly speaking, it doesn't predict secondary structure, but Rfam is useful for trying to predict the function of non-coding RNAs: http://rfam.sanger.ac.uk/

I'm sure there are a lot more, but these are the programs that I have experience with.

Answer 2

[laxvid]

Check out: http://selab.janelia.org/publications/Eddy13b/Eddy13b-preprint.pdf

Answer 3

[PoGibas]

Sveikas Tomai!

If you're looking for something new I would suggest this arxiv paper: RNA secondary structure prediction from multi-aligned sequences.

Sekmes

Answer 4

[Asaf]

Contrafold is another tool that doesn't use energy minimization but probabilistic methods.