I have the secondary structure of RNA in dot bracket notation and with the same dot bracket notation I need to calculate the free energy.
Could anyone suggest a tool, server or an algorithm to calculate the free energy from dot bracket notation of RNA?
You can use RNAeval webserver http://rna.tbi.univie.ac.at/cgi-bin/RNAeval.cgi. Simply introduce sequence and RNA structure in dot bracket notation and it will calculate energy. Alternatively use RNAstructure program http://rna.urmc.rochester.edu/RNAstructure.html. Fold RNA and check if the structure is the same. If not you can force single and double stranded regions in ,,force'' panel just before you click ,,fold as RNA''.
I am agree with Dr. Blaszczyk. You can use RNAeval webserver. Alternatively, you can use mfold Web Server (http://mfold.rna.albany.edu/?q=mfold).
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