user manuals

manual/readme.tex

@@ -40,7 +40,7 @@
 
 
 \begin{document} %%%% samotny dokument zacina tu %%%%
-\bibliographystyle{plainnat}
+\bibliographystyle{alpha}
 
 \begin{center}
 \section*{RNArobo 2.1.0 -- Quick Start Guide}
@@ -49,7 +49,7 @@ \section*{RNArobo 2.1.0 -- Quick Start Guide}
 
 RNArobo is a fast RNA structural motif search tool. RNArobo can search sequence databases in FASTA format for a motif defined by a ``descriptor'', which can specify primary and secondary structure constraints.
 
-The format of an RNArobo descriptor is an extension of the descriptor format used by RNABob (a search tool by \citet{eddy1996}), thus RNABob descriptors are compatible with RNArobo. A descriptor consists of three parts:
+The format of an RNArobo descriptor is an extension of the descriptor format used by RNABob \cite{eddy1996}, thus RNABob descriptors are compatible with RNArobo. A descriptor consists of three parts:
 \begin{enumerate}
 \item a \textbf{motif map} -- a list of individual \emph{structural elements}
   ordered from 5' to 3' end along the sequence
@@ -102,7 +102,7 @@ \section*{Example Descriptors}
 This variation of the previous descriptor allows only canonical base-pairs \texttt{A-T} and \texttt{C-G} in the relational element \texttt{r1}. The individual IUPAC codes in the \emph{transformation} string \texttt{TGCA} define nucleotides that can pair with \texttt{A}, \texttt{C}, \texttt{G}, and \texttt{T}, respectively in this order. For default helical elements (e.g. \texttt{h1}) RNArobo allows also Watson-Crick base pairs, as the default \emph{transformation} string is \texttt{TGYR}.
 \end{quote}
 
-(\textbf{Optional}) The last line of the example descriptor above illustrates usage of an optional reorder command which specifies the order in which elements are internally searched by the RNArobo algorithm, similarly to RNAMot \citep{gautheret1990}. If this command is absent or does not contain all elements, an automatic data-driven method is used to determine the best possible ordering of all remaining elements. This command has no principal impact on the actual results of the search, but defining a previously trained order can speed up the search by few seconds.
+(\textbf{Optional}) The last line of the example descriptor above illustrates usage of an optional reorder command which specifies the order in which elements are internally searched by the RNArobo algorithm, similarly to RNAMot \cite{gautheret1990}. If this command is absent or does not contain all elements, an automatic data-driven method is used to determine the best possible ordering of all remaining elements. This command has no principal impact on the actual results of the search, but defining a previously trained order can speed up the search by few seconds.
 
 \section*{Installation / Usage}
 To run RNArobo on your system, you need GCC C++ compiler (tested with version 4.4.5) or for 64-bit Linux systems we directly provide an executable binary.

manual/readme_ffilter.tex

@@ -0,0 +1,72 @@
+%
+%
+% Project      : RNA motif searching in genomic sequences
+% Description  : the LaTeX source code of the readme file
+%
+% Author       : Ladislav Rampasek <[email protected]>
+% Institution  : Comenius University in Bratislava
+%
+
+\documentclass[11pt]{article}
+%\topmargin=-2.5cm
+%\usepackage{a4wide}
+\usepackage{fullpage}
+\usepackage[english]{babel}
+\usepackage[IL2]{fontenc}
+\usepackage[utf8]{inputenc}
+\usepackage[none]{hyphenat}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{graphicx}
+\usepackage{float}
+\usepackage{enumitem}
+
+\usepackage{ifpdf}
+\ifpdf
+\usepackage{thumbpdf}
+\pdfcompresslevel=9
+\RequirePackage[colorlinks,hyperindex,plainpages=false]{hyperref}
+\def\pdfBorderAttrs{/Border [0 0 0] } % No border arround Links
+\else
+\RequirePackage[plainpages=true]{hyperref}
+\usepackage{color}
+\fi
+
+\usepackage{natbib}
+%\usepackage{xltxtra}
+%\setmainfont[Mapping=tex-text]{Ubuntu}
+\usepackage[all]{hypcap}
+
+
+\begin{document} %%%% samotny dokument zacina tu %%%%
+\bibliographystyle{alpha}
+
+\begin{center}
+\section*{Fold-Filter \& scripts -- User Manual}
+\today
+\end{center}
+
+Description about what it does and what is it good for.
+
+Explanation of the filtering options and of the filter format.
+
+\section*{Example Filter}
+More detailed explanation on examples.
+
+\section*{Installation / Usage}
+Mainly discuss all the prerequisites that are needed - Python2.x, Perl, ViennaRNA \cite{lorenz2011viennarna}, DotKnot \cite{sperschneider2010dotknot, sperschneider2011heuristic} with its own custom ViennaRNA instance, optionally UCLUST \cite{edgar2010search}.
+
+\setdescription{leftmargin=\parindent,labelindent=\parindent}
+\subsection*{Available Options:}
+..options..
+
+\section*{More Scripts}
+Short description of the other scripts.
+\subsection*{parse\_rnarobo.pl}
+\subsection*{weights\_tool.pl}
+
+\section*{Example Usage in Pipeline with RNArobo}
+
+\bibliography{ref}
+
+\end{document}

manual/ref.bib

@@ -210,4 +210,50 @@ @misc{intro2001
   title={{A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays}},
   howpublished={"\url{http://www.ebi.ac.uk/microarray/biology_intro.html}", European Bioinformatics Institute},
   year={2001}
-}
+}
+
+@article{sperschneider2010dotknot,
+  title={{DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model}},
+  author={Sperschneider, Jana and Datta, Amitava},
+  journal={Nucleic acids research},
+  volume={38},
+  number={7},
+  pages={e103--e103},
+  year={2010},
+  publisher={Oxford Univ Press}
+}
+
+@article{sperschneider2011heuristic,
+  title={{Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins}},
+  author={Sperschneider, Jana and Datta, Amitava and Wise, Michael J},
+  journal={RNA},
+  volume={17},
+  number={1},
+  pages={27--38},
+  year={2011},
+  publisher={Cold Spring Harbor Lab}
+}
+
+@article{lorenz2011viennarna,
+  title={{ViennaRNA Package 2.0}},
+  author={Lorenz, Ronny and Bernhart, Stephan HF and Zu Siederdissen, Christian Hoener and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L and others},
+  journal={Algorithms for Molecular Biology},
+  volume={6},
+  number={1},
+  pages={26},
+  year={2011}
+}
+
+@article{edgar2010search,
+  title={{Search and clustering orders of magnitude faster than BLAST}},
+  author={Edgar, Robert C},
+  journal={Bioinformatics},
+  volume={26},
+  number={19},
+  pages={2460--2461},
+  year={2010},
+  publisher={Oxford Univ Press}
+}
+
+
+