Modules

Here is a list of all modules:

• RNA Secondary Structure Folding
  • Calculating Minimum Free Energy (MFE) Structures
    • 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
  • Calculating Partition Functions and Pair Probabilities
    • Compute the structure with maximum expected accuracy (MEA)
    • Compute the centroid structure
    • Partition Function for two hybridized Sequences
    • Partition Function for two hybridized Sequences 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
  • 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
  • Calculate Secondary Structures of two RNAs upon Dimerization
    • MFE Structures of two hybridized Sequences
    • Partition Function for two hybridized Sequences
    • Partition Function for two hybridized Sequences as a stepwise Process
  • Predicting Consensus Structures from Alignment(s)
    • 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
    • Reading/Writing energy parameter sets from/to File
      • Converting energy parameter files
  • Energy evaluation
  • Searching Sequences for Predefined Structures
  • Classified Dynamic Programming
    • Distance based partitioning of the Secondary Structure Space
      • Calculating MFE representatives of a Distance Based Partitioning
      • Calculate Partition Functions of a Distance Based Partitioning
      • Stochastic Backtracking of Structures from Distance Based Partitioning
    • Compute the Density of States
• Parsing and Comparing - Functions to Manipulate Structures