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

   1 \hypertarget{group__consensus__mfe__fold}{\section{M\-F\-E Consensus Structures for Sequence Alignment(s)}
   2 \label{group__consensus__mfe__fold}\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
   3 }
   4 Collaboration diagram for M\-F\-E Consensus Structures for Sequence Alignment(s)\-:
   5 \nopagebreak
   6 \begin{figure}[H]
   7 \begin{center}
   8 \leavevmode
   9 \includegraphics[width=350pt]{group__consensus__mfe__fold}
  10 \end{center}
  11 \end{figure}
  12 \subsection*{Functions}
  13 \begin{DoxyCompactItemize}
  14 \item
  15 float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
  16 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item
  17 float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
  18 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item
  19 \hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}
  20
  21 \begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\end{DoxyCompactItemize}
  22
  23
  24 \subsection{Detailed Description}
  25
  26
  27 \subsection{Function Documentation}
  28 \hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!alifold@{alifold}}
  29 \index{alifold@{alifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
  30 \subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (
  31 \begin{DoxyParamCaption}
  32 \item[{const char $\ast$$\ast$}]{strings, }
  33 \item[{char $\ast$}]{structure}
  34 \end{DoxyParamCaption}
  35 )}}\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}
  36
  37
  38 Compute M\-F\-E and according consensus structure of an alignment of sequences.
  39
  40 This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.
  41
  42 Sufficient space must be allocated for 'structure' before calling \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()}.
  43
  44
  45 \begin{DoxyParams}{Parameters}
  46 {\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
  47 \hline
  48 {\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\
  49 \hline
  50 \end{DoxyParams}
  51 \begin{DoxyReturn}{Returns}
  52 The free energy score in kcal/mol
  53 \end{DoxyReturn}
  54 \hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!circalifold@{circalifold}}
  55 \index{circalifold@{circalifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
  56 \subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (
  57 \begin{DoxyParamCaption}
  58 \item[{const char $\ast$$\ast$}]{strings, }
  59 \item[{char $\ast$}]{structure}
  60 \end{DoxyParamCaption}
  61 )}}\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}
  62
  63
  64 Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear.
  65
  66
  67 \begin{DoxyParams}{Parameters}
  68 {\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
  69 \hline
  70 {\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\
  71 \hline
  72 \end{DoxyParams}
  73 \begin{DoxyReturn}{Returns}
  74 The free energy score in kcal/mol
  75 \end{DoxyReturn}