Modules

Here is a list of all modules:

[detail level 1234]

RNA Secondary Structure Folding	This module contains all functions related to thermodynamic folding of RNAs
Calculating Minimum Free Energy (MFE) Structures	This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences
MFE Structures of two hybridized Sequences
MFE Consensus Structures for Sequence Alignment(s)
Local MFE structure Prediction and Z-scores
Calculating MFE representatives of a Distance Based Partitioning	Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures
Calculating Partition Functions and Pair Probabilities	This section provides information about all functions and variables related to the calculation of the partition function and base pair probabilities
Compute the structure with maximum expected accuracy (MEA)
Compute the centroid structure
Partition Function for two hybridized Sequences	Partition Function Cofolding
Partition Function for two hybridized Sequences as a stepwise Process	Partition Function Cofolding as a stepwise process
Partition Function and Base Pair Probabilities for Sequence Alignment(s)
Partition functions for locally stable secondary structures
Calculate Partition Functions of a Distance Based Partitioning	Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures
Enumerating Suboptimal Structures
Suboptimal structures according to Zuker et al. 1989
Suboptimal structures within an energy band arround the MFE
Stochastic backtracking in the Ensemble
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
Stochastic Backtracking of Structures from Distance Based Partitioning	Contains functions related to stochastic backtracking from a specified distance class
Calculate Secondary Structures of two RNAs upon Dimerization	Predict structures formed by two molecules upon hybridization
MFE Structures of two hybridized Sequences
Partition Function for two hybridized Sequences	Partition Function Cofolding
Partition Function for two hybridized Sequences as a stepwise Process	Partition Function Cofolding as a stepwise process
Predicting Consensus Structures from Alignment(s)	Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
MFE Consensus Structures for Sequence Alignment(s)
Partition Function and Base Pair Probabilities for Sequence Alignment(s)
Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
Local MFE consensus structures for Sequence Alignments
Predicting Locally stable structures of large sequences
Local MFE structure Prediction and Z-scores
Partition functions for locally stable secondary structures
Local MFE consensus structures for Sequence Alignments
Change and Precalculate Energy Parameter Sets and Boltzmann Factors	All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s)
Reading/Writing energy parameter sets from/to File	Read and Write energy parameter sets from and to text files
Converting energy parameter files	Convert energy parameter files into the latest format
Energy evaluation	This module contains all functions and variables related to energy evaluation of sequence/structure pairs
Searching Sequences for Predefined Structures
Classified Dynamic Programming
Distance based partitioning of the Secondary Structure Space	Compute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space
Calculating MFE representatives of a Distance Based Partitioning	Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures
Calculate Partition Functions of a Distance Based Partitioning	Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures
Stochastic Backtracking of Structures from Distance Based Partitioning	Contains functions related to stochastic backtracking from a specified distance class
Compute the Density of States
Parsing and Comparing - Functions to Manipulate Structures