I would use RNAfold from the Vienna RNA package which works for DNA too : http://rna.tbi.univie.ac.at/. You can either call the program from Perl or make a Perl version of the available source code.

As far as I can remember, you just supply a FASTA file and you will get dG and other thermodynamic values for each of your sequences.

Try using RNAplfold from the same package, it predicts stable local structures that you can obtain from the dot-plot or use the -u option to get the probability for a region being unpaired. You can run the program and then use perl to digest the output

Hi There,

If you are interested in more detailed information about the hairpin, there is a script on this page that will parse the RNAFold output. It may be a little buggy but it has worked for me in the past. RNA fold Topic

I ended up writing a wrapper/parser in Perl for the commandline executed RNAstructure package (University of Rochester) althought it's abit of a hack it works really well for my purposes.

The script takes a multiple sequence FASTA file and processes each sequence with fold.exe of the package. The results are gathered in dot.bracket FASTA file. From this, postscript images are created, depicting the predicted structure(s). Cutoff can be manually set to obtain only the structures with the highest likelyhood. All postscript files are gathered and output is combined into a single PDF-file using Ghostscript.

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