readme_ffilter.tex

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% Project      : RNA motif searching in genomic sequences
% Description  : the LaTeX source code of the readme file
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% Author       : Ladislav Rampasek <rampasek@gmail.com>
% Institution  : Comenius University in Bratislava
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\section*{Fold-Filter \& scripts -- User Manual}
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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}.

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\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}

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