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.
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tomas.iesmantas •
4 answers
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.
Sveikas Tomai!
If you're looking for something new I would suggest this arxiv paper: RNA secondary structure prediction from multi-aligned sequences.
Sekmes
Contrafold is another tool that doesn't use energy minimization but probabilistic methods.
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