\documentclass[a4paper]{article}

\usepackage{graphics}

\title{GeneRfold Package}
\author{ A. Lucas, C. Thermes \& Y. d'Aubenton-Carafa}

%\VignetteIndexEntry{Introduction to GeneR}
%\VignettePackage{GeneR}
\SweaveOpts{echo=FALSE}
\usepackage{a4wide}

\begin{document}

\maketitle

\tableofcontents

\section{Overview}

GeneRfold allows the use of Vienna RNA library within R.

The Vienna RNA library propose some tools for the prediction and comparison of RNA secondary structures.


\section{Main functions}

\subsection{Fold routine}

  Folds the sequence and returns the minimum free energyin kcal/mol; the
  mfe structure in bracket notation is returned.

<<echo=TRUE>>=
library(GeneRfold)
s <- "TTAGCTCAATTGGTAAAGACCCTAGGCGAAGCTTAGAGGTCGCCGGTT"
fold(s)
@ 

\subsection{Plot routine}

 Plot (to a postcript file) a structure (rnaPlot) made by fold
  or the dot plot.

<<echo=TRUE>>=
s <- "TTAGCTCAATTGGTAAAGACCCTAGGCGAAGCTTAGAGGTCGCCGGTT"
dotPlot(s,file="dot.ps")
rnaPlot(s,file="rna.ps")
@ 

\begin{figure}
\resizebox{\textwidth}{!}{\includegraphics{rnafold}}
\caption{Plot routine}
\label{plot}
\end{figure}



\end{document}