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 |