binaries/src/ViennaRNA/doc/latex/modules.tex

   1 \section{Modules}
   2 Here is a list of all modules:\begin{DoxyCompactList}
   3 \item \contentsline{section}{RNA Secondary Structure Folding}{\pageref{group__folding__routines}}{}
   4 \begin{DoxyCompactList}
   5 \item \contentsline{section}{Calculating Minimum Free Energy (MFE) Structures}{\pageref{group__mfe__fold}}{}
   6 \begin{DoxyCompactList}
   7 \item \contentsline{section}{MFE Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
   8 \item \contentsline{section}{MFE Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
   9 \item \contentsline{section}{Local MFE structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
  10 \item \contentsline{section}{Calculating MFE representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
  11 \end{DoxyCompactList}
  12 \item \contentsline{section}{Calculating Partition Functions and Pair Probabilities}{\pageref{group__pf__fold}}{}
  13 \begin{DoxyCompactList}
  14 \item \contentsline{section}{Compute the structure with maximum expected accuracy (MEA)}{\pageref{group__mea__fold}}{}
  15 \item \contentsline{section}{Compute the centroid structure}{\pageref{group__centroid__fold}}{}
  16 \item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
  17 \item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
  18 \item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
  19 \item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
  20 \item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
  21 \end{DoxyCompactList}
  22 \item \contentsline{section}{Enumerating Suboptimal Structures}{\pageref{group__subopt__fold}}{}
  23 \begin{DoxyCompactList}
  24 \item \contentsline{section}{Suboptimal structures according to Zuker et al. 1989}{\pageref{group__subopt__zuker}}{}
  25 \item \contentsline{section}{Suboptimal structures within an energy band arround the MFE}{\pageref{group__subopt__wuchty}}{}
  26 \item \contentsline{section}{Stochastic backtracking in the Ensemble}{\pageref{group__subopt__stochbt}}{}
  27 \begin{DoxyCompactList}
  28 \item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
  29 \item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
  30 \end{DoxyCompactList}
  31 \end{DoxyCompactList}
  32 \item \contentsline{section}{Calculate Secondary Structures of two RNAs upon Dimerization}{\pageref{group__cofold}}{}
  33 \begin{DoxyCompactList}
  34 \item \contentsline{section}{MFE Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
  35 \item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
  36 \item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
  37 \end{DoxyCompactList}
  38 \item \contentsline{section}{Predicting Consensus Structures from Alignment(s)}{\pageref{group__consensus__fold}}{}
  39 \begin{DoxyCompactList}
  40 \item \contentsline{section}{MFE Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
  41 \item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
  42 \item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
  43 \item \contentsline{section}{Local MFE consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
  44 \end{DoxyCompactList}
  45 \item \contentsline{section}{Predicting Locally stable structures of large sequences}{\pageref{group__local__fold}}{}
  46 \begin{DoxyCompactList}
  47 \item \contentsline{section}{Local MFE structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
  48 \item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
  49 \item \contentsline{section}{Local MFE consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
  50 \end{DoxyCompactList}
  51 \item \contentsline{section}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{\pageref{group__energy__parameters}}{}
  52 \begin{DoxyCompactList}
  53 \item \contentsline{section}{Reading/Writing energy parameter sets from/to File}{\pageref{group__energy__parameters__rw}}{}
  54 \begin{DoxyCompactList}
  55 \item \contentsline{section}{Converting energy parameter files}{\pageref{group__energy__parameters__convert}}{}
  56 \end{DoxyCompactList}
  57 \end{DoxyCompactList}
  58 \item \contentsline{section}{Energy evaluation}{\pageref{group__eval}}{}
  59 \item \contentsline{section}{Searching Sequences for Predefined Structures}{\pageref{group__inverse__fold}}{}
  60 \item \contentsline{section}{Classified Dynamic Programming}{\pageref{group__class__fold}}{}
  61 \begin{DoxyCompactList}
  62 \item \contentsline{section}{Distance based partitioning of the Secondary Structure Space}{\pageref{group__kl__neighborhood}}{}
  63 \begin{DoxyCompactList}
  64 \item \contentsline{section}{Calculating MFE representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
  65 \item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
  66 \item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
  67 \end{DoxyCompactList}
  68 \item \contentsline{section}{Compute the Density of States}{\pageref{group__dos}}{}
  69 \end{DoxyCompactList}
  70 \end{DoxyCompactList}
  71 \item \contentsline{section}{Parsing and Comparing -\/ Functions to Manipulate Structures}{\pageref{group__parse}}{}
  72 \end{DoxyCompactList}