%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% PATTERN COMPARISONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Pattern comparisons}

\textbf{TO BE WRITTEN}

\section{Comparing patterns with patterns}

\begin{small}
\begin{verbatim}
compare-patterns

\end{verbatim}
\end{small}

\section{Comparing discovered patterns wirth a library of TF-binding consensus}

Let us suppose that we dispose of a collection of experimentally
characterized binding consensus for the organism of interest, in a
file called \file{known\_consensus.pat}. 

\begin{small}
\begin{verbatim}
compare-patterns -v 1 \
  -file1 dyads.tab \
  -file2 RegulonDB_sites.tab \
  -return weight,offset,strand,length,Pval,Eval_p,sig_p,Eval_f,sig_f,id,seq \
  -2str -lth weight 6 \
  -o dyads_vs_RegulonDB.tab
\end{verbatim}
\end{small}
