Index

Symbols | _ | A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | V

Symbols

  • (Tertiary) Structure Motifs

_

A

  • Additional Utilities

B

  • Basic Data Structures
  • Bibliography

C

  • C Examples
  • Calculate Partition Functions of a Distance Based Partitioning
  • Calculating MFE representatives of a Distance Based Partitioning
  • Callback Functions
  • Changelog
  • Classified DP variations
  • Classified Dynamic Programming variants
  • Comparative Structure Prediction
  • Comparative structure prediction
  • Complex structured modules
  • Compute the centroid structure
  • Compute the Density of States
  • Compute the structure with maximum expected accuracy (MEA)
  • Concepts and Algorithms
  • constrain
  • Constraining the RNA folding grammar
  • Converting Energy Parameter Files
  • COORDINATE

D

  • Data Structures and Preprocessor Macros
  • Deprecated List
  • Direct refolding paths between two secondary structures
  • Distance based partitioning of the Secondary Structure Space

E

  • Examples
  • Experimental Structure Probing Data
  • Experimental structure probing data
  • Extending the folding grammar with additional domains

F

  • File Formats
  • Fine-tuning of the implemented models
  • Free energy evaluation
  • Free Energy of Secondary Structures
  • Functions for Creating Secondary Structure Plots, Dot-Plots, and More
  • Functions that provide dynamically buffered stream-like data structures
  • Functions to convert between various units
  • Functions to generate annotations for Secondary Structure Plots, Dot-Plots, and Others
  • Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments

G

H

  • HelloWorld (Perl/Python)

I

  • I/O Formats
  • Incorporating ligands binding to specific sequence/structure motifs using soft constraints
  • Installation and Configuration

L

  • Ligand Binding
  • Ligands binding to RNA structures
  • Local MFE Consensus Structure Prediction for Sequence Alignments
  • Local MFE Structure Prediction and Z-scores
  • Locally Stable Secondary Structures
  • Locally stable structures

M

  • MFE Consensus Structures for Sequence Alignment(s)
  • MFE Structures of single Nucleic Acid Sequences
  • MFE Structures of two hybridized Sequences
  • Minimum Free Energy (MFE) algorithms
  • Minimum Free Energy Algorithm(s)
  • Model Details
  • MOVE_TYPE

N

  • namespace
  • Neighborhood relation and move sets for secondary structures

P

  • parset
  • Parsing, converting, and comparing sequences
  • Parsing, converting, comparing secondary structures
  • Partition Function and Base Pair Probabilities for Sequence Alignment(s)
  • Partition Function and Equilibrium Probabilities for Locally Stable Secondary Structures
  • Partition Function and Equilibrium Probabilitiy Algorithm(s)
  • Partition function and equilibrium properties
  • Partition Function for two hybridized Sequences
  • Partition Function for two hybridized Sequences as a stepwise Process
  • Perl5 Examples
  • Plotting
  • Postorder_list
  • Process and evaluate individual loops
  • pu_contrib
  • pu_out
  • Python Examples

R

  • Reading/Writing Energy Parameter Sets from/to File
  • Refolding paths of secondary structures
  • RNA Secondary Structure Landscapes
  • RNA Sequence Design
  • RNA Structure
  • RNA Structure Notations
  • RNA-RNA Interaction
  • RNA-RNA interaction
  • RNAlib API v3.0
  • RNAlib-2.4.6

S

  • Structure sampling from the ensemble
  • Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989
  • Suboptimal structures within an energy band arround the MFE
  • Suboptimals and (other) Representative Structures
  • Suboptimals and representative structures
  • swString

T

  • The 'Fold Compound'
  • The Dynamic Programming Matrices
  • The Fold Compound
  • The RNA folding grammar

U

  • Utilities for sequence alignments

V