Structure analysis

• Secondary structure
• Tertiary structure

• Secondary structure




MFOLD

• mfold: Prediction of RNA Secondary Structure by Energy Minimization.




PREDATOR

• predator: Protein secondary structure prediction from sequences.




TOPPRED

• toppred: Topology prediction of membrane proteins.




VIENNARNA

• rnaalifold: Calculate secondary structures for a set of aligned RNAs
• rnaduplex: Compute the structure upon hybridization of two RNA strands
• rnafold: Calculate secondary structures of RNAs.
• rnacofold: Calculate secondary structures of two RNAs with dimerization
• rnalfold: Calculate locally stable secondary structures of RNAs.
• rnaplfold: Compute average pair probabilities for local base pairs in long sequences.
• rnaeval: Calculate energy of RNA sequences on given secondary structure.
• rnadistance: Calculate distances of RNA secondary structures.
• rnapdist: Calculate distances of thermodynamic RNA secondary structures ensembles.
• rnainverse: Find RNA sequences with given secondary structure.
• rnasubopt: Calculate suboptimal secondary structures of RNAs.




EMBOSS

• garnier: Predicts protein secondary structure
• helixturnhelix: Report nucleic acid binding motifs.
• hmoment: Hydrophobic moment calculation
• pepcoil: Predicts coiled coil regions.
• pepnet: Displays proteins as a helical net.
• pepwheel: Shows protein sequences as helices.
• tmap: Displays membrane spanning regions.

• Tertiary structure

COSA

• cosa: Clustal Ouput Structural Analysis.