NUCLEIC RNA FOLDING

 

RNA folding methods and analysis

Program nameDescription
ovrnaalifold Calculate secondary structures for a set of aligned RNAs
ovrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partition)
ovrnacofold Calculate secondary structures of RNA dimers
ovrnacofoldconc Calculate secondary structures of RNA dimers (concentrations)
ovrnacofoldpf Calculate secondary structures of RNA dimers (partitioning)
ovrnadistance Calculate distances between RNA secondary structures
ovrnaduplex Predict RNA duplex (hybridization) sites and structure
ovrnaeval Calculate energy of RNA sequences with a given secondary structure
ovrnaevalpair Calculate energy of RNA sequences on given secondary structure
ovrnafold Calculate min. energy RNA structure / pair probabilities (partition)
ovrnafoldpf Calculate min. energy RNA structure / pair probabilities
ovrnaheat Calculate specific heat of RNA melting
ovrnainverse Find RNA sequences with a given secondary structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Draw RNA secondary structures
ovrnasubopt Calculate suboptimal secondary structure of RNA
vrna2dfold Calculate RNA structures and samples of k,l neighbourhoods
vrnaaliduplex RNA duplex calculation for two sequence alignments
vrnaalifold Calculate secondary structures for a set of aligned RNAs
vrnaalifoldpf Calculate secondary structures for a set of aligned RNAs (partition)
vrnacofold Calculate secondary structures of RNA dimers
vrnacofoldconc Calculate secondary structures of RNA dimers (concentrations)
vrnacofoldpf Calculate secondary structures of RNA dimers (partitioning)
vrnadistance Calculate distances between RNA secondary structures
vrnaduplex Predict RNA duplex (hybridization) sites and structure
vrnaeval Calculate energy of RNA sequences with a given secondary structure
vrnaevalpair Calculate energy of RNA sequences on given secondary structure
vrnafold Calculate min. energy RNA secondary structures and pair probabilities
vrnafoldpf Calculate min. energy RNA structures / pair probabilities (partition)
vrnaheat Calculate specific heat of RNA melting
vrnainverse Find RNA sequences with a given secondary structure
vrnalalifoldpf Calculate secondary structures for a set of aligned RNAs (partition)
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Calculate locally stable secondary structures of RNAs plus zscore
vrnapkplex Calculate RNA structures plus pseudoknots
vrnaplfold Compute avg. pair probabilities for local base pairs in RNA sequences
vrnaplot Draw RNA secondary structures
vrnasubopt Calculate suboptimal secondary structures of RNAs