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	Finds inverted repeats in nucleotide sequences
sirna	Finds siRNA duplexes in mRNA
ovrnaalifold	RNA alignment folding
ovrnaalifoldpf	RNA alignment folding with partition
ovrnacofold	RNA cofolding
ovrnacofoldconc	RNA cofolding with concentrations
ovrnacofoldpf	RNA cofolding with partitioning
ovrnadistance	RNA distances
ovrnaduplex	RNA duplex calculation
ovrnaeval	RNA eval
ovrnaevalpair	RNA eval with cofold
ovrnafold	Calculate secondary structures of RNAs
ovrnafoldpf	Secondary structures of RNAs with partition
ovrnaheat	RNA melting
ovrnainverse	RNA sequences matching a structure
ovrnalfold	Calculate locally stable secondary structures of RNAs
ovrnaplot	Plot vrnafold output
ovrnasubopt	Calculate RNA suboptimals
vrna2dfold	Structures and samples of k,l neighbourhoods
vrnaaliduplex	RNA duplex calculation for two sequence alignments
vrnaalifold	RNA alignment folding
vrnaalifoldpf	RNA alignment folding with partition
vrnacofold	RNA cofolding
vrnacofoldconc	RNA cofolding with concentrations
vrnacofoldpf	RNA cofolding with partitioning
vrnadistance	RNA distances
vrnaduplex	RNA duplex calculation
vrnaeval	RNA eval
vrnaevalpair	RNA eval with cofold
vrnafold	Calculate secondary structures of RNAs
vrnafoldpf	Secondary structures of RNAs with partition
vrnaheat	RNA melting
vrnainverse	RNA sequences matching a structure
vrnalalifoldpf	Locally stable 2ry structures for a set of aligned RNAs
vrnalfold	Calculate locally stable secondary structures of RNAs
vrnalfoldz	Locally stable secondary structures of RNAs plus zscore
vrnapkplex	RNA structures plus pseudoknots
vrnaplfold	Locally stable RNA 2ry structures - pair probabilities
vrnaplot	Plot vrnafold output
vrnasubopt	Calculate RNA suboptimals