EMBOSS

| 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