NUCLEIC 2D STRUCTURE

Nucleic acid secondary structure

Program name	Description
banana	Plot bending and curvature data for B-DNA
btwisted	Calculate the twisting in a B-DNA sequence
einverted	Find inverted repeats in nucleotide sequences
sirna	Find siRNA duplexes in mRNA
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