RNAlib-2.2.7
Modules
Here is a list of all modules:
[detail level 1234]
 RNA Secondary Structure PredictionThis module contains all functions related to thermodynamic folding of RNAs
 Computing Minimum Free Energy (MFE) StructuresThis section covers all functions and variables related to the calculation of minimum free energy (MFE) structures
 MFE Structures of single Nucleic Acid SequencesThis 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 PartitioningCompute 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 ProbabilitiesThis 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 SequencesPartition Function Cofolding
 Partition Function for two hybridized Sequences as a stepwise ProcessPartition 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 PartitioningCompute 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 PartitioningContains functions related to stochastic backtracking from a specified distance class
 Calculate Secondary Structures of two RNAs upon DimerizationPredict structures formed by two molecules upon hybridization
 MFE Structures of two hybridized Sequences
 Partition Function for two hybridized SequencesPartition Function Cofolding
 Partition Function for two hybridized Sequences as a stepwise ProcessPartition 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 SpaceCompute Thermodynamic properties for a Distance Class Partitioning of the Secondary Structure Space
 Calculating MFE representatives of a Distance Based PartitioningCompute 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 PartitioningCompute 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 PartitioningContains 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 structuresImplementation of heuristics to explore optimal (re-)folding paths between two secondary structures
 Free Energy Evaluation for given Sequence / Structure PairsThis module contains all functions and variables related to energy evaluation of sequence/structure pairs
 Processing and Evaluating Decomposed Loops
 Energy Parameter Sets and Boltzmann FactorsAll 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 FileRead and Write energy parameter sets from and to text files
 Converting Energy Parameter FilesConvert energy parameter files into the latest format
 Manipulation of the Prediction Models
 Constraining the Secondary Structure Predictions and EvaluationsThis module covers all functions and variables related to the problem of incorporating secondary structure constraints into the folding recursions
 Hard ConstraintsThis module covers all functionality for hard constraints in secondary structure prediction
 Soft ConstraintsFunctions and data structures for secondary structure soft constraints
 Incorporating SHAPE reactivity dataIncorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints
 Incorporating ligands binding to specific sequence/structure motifsThis 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 dataFind 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 MacrosAll datastructures and typedefs shared among the Vienna RNA Package can be found here
 The Fold CompoundThis 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 MatricesThis 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