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1 parent c8e81ad commit cf17bd46bc9ba414a45917a2823748a35b6b5e34 @vreinharz vreinharz committed Oct 6, 2012
Showing with 9 additions and 5 deletions.
  1. +9 −5 Recomb/introduction_RECOMB.tex
@@ -27,13 +27,14 @@ \section{Introduction}
evolution~\cite{Zuckerkandl1965}, and with all their characteristics, rRNAs have
become a prime candidate for phylogenetic studies~\cite{Olsen1986, Olsen1993}.
-In this paper, we tackle the problem of exploring an rRNA sequence mutant space, to
-identify positions which are probably sequencing error, given the rRNA family sequences
-and its consensus structure.
+In this paper, we tackle the problem of, given an rRNA sequence its family and
+consensus secondary structure,
+identifing the positions which are probably sequencing error.
Leveraging the techniques in \texttt{RNAmutants}~\cite{Waldispuhl2008}, and building on top
of the \emph{Inside-Outside algorithm}, we define here a new method called \texttt{RNApyro}
-efficiently computing for large RNAs those probabilities.
+efficiently computing for large RNAs those probabilities under a new
+pseudo-energetic model.
Classical techniques define a probabilistic model using a Boltzmann distribution
whose weights are based on the free energy of the structure, using as energy parameter
the values of Turner found in the NNDB~\cite{Turner2010} for stacked,
@@ -44,4 +45,7 @@ \section{Introduction}
define an isostericity distance, increasing as two base pairs differ
more from one another in space. We incorporate this second measure in the Boltzmann weights.
-To benchmark
+To benchmark our technique we use the 5S ribosomal RNA family,
+ which is around $120$ nucleotides longs. We show

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