Programs for RNA secondary structure predictions

Question

[torkel.loman]

I am basically looking for recommendations for programs that can predict RNA secondary structure.

I wrote one myself using the Zucker algorithm, but it was mostly as an exercise and I understand there are better available.

The one that I know about is HotKnot (http://www.ncbi.nlm.nih.gov/pubmed/16199760 , able to do pseudoknots) but it is 10 years old by now and I have not found much else on it except for the original paper.

I found another, Hfold (http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-147) which also claims to handle pseudoknots with good results in good time. It requires a structure in the input though.

Also, anyone have any input on programs that are good (and fast) for non pseudoknot structures+

Would be happy if someone had some input.

[Asaf]

Vienna RNA package (no pseudoknots) or Mfold

Answer 1

[Carlo Yague]

There is RNA fold, which computes the minimum free energy and backtraces an optimal secondary structure(1). It is fast an easy to use and from 2011.

(1) Lorenz, R. and Bernhart, S.H. and Höner zu Siederdissen, C. and Tafer, H. and Flamm, C. and Stadler, P.F. and Hofacker, I.L. "ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6:1 page(s): 26, 2011

[pradyumna Jayaram]

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

Answer 2

[Medhat]

List of some programs

https://omictools.com/rna-structurome-category

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

for me I used Mfold before

Answer 3

[fanli.gcb]

I'll add that RNAstructure incorporates experimental constraint data (e.g. SHAPE): http://rna.urmc.rochester.edu/RNAstructure.html

Answer 4

[torkel.loman]

Thank you very much, I'm looking into the alternatives but they seems good.

Answer 5

[Erik Wright]

Consensus RNA secondary structure can be predicted from a sequence alignment using the DECIPHER package for R:

rna <- readRNAStringSet("<<path to FASTA file>>")
?PredictDBN # opens helpful information
p <- PredictDBN(rna, "states")

I hope that helps!