This is E's modified version of RNAstructure. ## RNAstructure data tables notes - rna.coaxial - rna.coaxstack - rna.cov - rna.dangle - rna.dynalignmiscloop - rna.helix_ends Table for terminal end penalties (e.g. AU/GU penalties). - rna.hexaloop Special hairpin loops of length 6. AU/GU penalties baked in. - rna.int11 1x1 special internal loops. AU/GU penalties baked in. - rna.int21 2x1 special internal loops. AU/GU penalties baked in. - rna.int22 2x2 special internal loops. AU/GU penalties baked in. - rna.loop - rna.miscloop - rna.param_map - rna.stack Stacking parameters for helices. - rna.tloop Special hairpin loops of length 4. AU/GU penalties baked in. - rna.triloop Special hairpin loops of length 3. AU/GU penalties baked in. - rna.tstack - rna.tstackcoax - rna.tstackh Hairpin loop terminal mismatch parameters. AU/GU penalties and other special hairpin parameters baked in. - rna.tstacki Internal loop terminal mismatch parameters. Internal loop AU/GU penalties baked in. - rna.tstacki1n Bulge loop terminal mismatch parameters. AU/GU penalties baked in. - rna.tstacki23 2x3 internal loop terminal mismatch parameters. Internal loop AU/GU penalties baked in. - rna.tstackm Below follows the original readme text of RNAstructure. ---- This is the source code for RNAstructure, which includes tools for RNA secondary structure prediction and analysis. It is covered by the GNU GENERAL PUBLIC LICENSE Version 2 (see gpl.txt for the full license). ---- Documentation and help can be accessed by opening the local file 'Index.html' from inside the 'manual/html' directory. It can also be found online at: http://rna.urmc.rochester.edu/RNAstructureHelp.html ---- Please contact David Mathews with any question or comments: David_Mathews@urmc.rochester.edu