I'm interested in prediction of hairpin structures from a large set of DNA sequences (fasta), which I extracted using my own perl scripts.
I'm looking for a tool that creates predictions of secondary structure (e.g. hairpin loops), and gives me some basic information such as free energy.
output should preferably in dot.bracket FASTA fileformat, so I can easily visualize the structures with known tools.
My weapons of choice would be either Perl or R. (I'm struggling with Taverna)
thanks in advance!