▼RNA Secondary Structure Prediction | This module contains all functions related to thermodynamic folding of RNAs |
▼Computing Minimum Free Energy (MFE) Structures | This section covers all functions and variables related to the calculation of minimum free energy (MFE) structures |
MFE Structures of single Nucleic Acid Sequences | 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 |
▼Computing 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 | |
▼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 | |
Inverse Secondary Structure Prediction | |
▼Refolding paths between secondary structues | |
Direct refolding paths between two secondary structures | Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures |
Free Energy Evaluation for given Sequence / Structure Pairs | This module contains all functions and variables related to energy evaluation of sequence/structure pairs |
Processing and Evaluating Decomposed Loops | |
▼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 |
Manipulation of the Prediction Models | |
▼Constraining the Secondary Structure Predictions and Evaluations | This module covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions |
Hard Constraints | This module covers all functionality for hard constraints in secondary structure prediction |
Soft Constraints | Functions and data structures for secondary structure soft constraints |
Incorporating SHAPE reactivity data | Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints |
Incorporating ligands binding to specific sequence/structure motifs | This module covers functions that enable the incorporation of ligand binding free energies to specific hairpin/interior loop motifs by means of generic soft constraints |
Generate soft constraints from data | Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments |
▼Data Structures and Preprocessor Macros | All datastructures and typedefs shared among the Vienna RNA Package can be found here |
The Fold Compound | This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib |
The Dynamic Programming Matrices | This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib |
▼Utilities | |
Parsing, Converting, and Comparing - Functions to Manipulate Sequence and Structure Strings | |
Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures | |
Various utilities for Sequence Alignments, and Comparative Structure Prediction | |
Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments | |
Functions for Creating RNA Secondary Structures Plots, Dot-Plots, and More | |