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vreinharz committed Oct 6, 2012
1 parent 2ff0683 commit 599f3a94a155e65d255c045012da2403fe10fab1
Showing with 24 additions and 4 deletions.
  1. +14 −0 Recomb/RNApyro.bib
  2. +9 −3 Recomb/introduction_RECOMB.tex
  3. +1 −1 Recomb/main_RECOMB.tex
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@@ -194,3 +194,17 @@ @article{Leontis2001
volume = {7},
year = {2001}
}
+Automatically generated by Mendeley 1.6
+Any changes to this file will be lost if it is regenerated by Mendeley.
+
+@article{Hori1987,
+author = {Hori, H and Osawa, S},
+file = {:Users/zenon/Documents/Mendeley/Hori, Osawa/1987/Molecular biology and evolution/Hori, Osawa\_1987\_Origin and Evolution of Organisms as Deduced from 5s Ribosomal RNA Sequences ’.pdf:pdf},
+journal = {Molecular biology and evolution},
+number = {5},
+pages = {445--472},
+title = {{Origin and Evolution of Organisms as Deduced from 5s Ribosomal RNA Sequences}},
+url = {http://mbe.oxfordjournals.org/content/4/5/445.short},
+volume = {4},
+year = {1987}
+}
@@ -44,7 +44,13 @@ \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.
+The 5S ribosomal RNA family, $119$ nucleotides long, was used to benchmark our method.
+It is a prime example since it has been extensively used for phylogenetic
+reconstructions~\cite{Hori1987} and its sequence has been recovered for over 8000 species
+ (RFAM Id: \texttt{RF00001}).
+ Using a leave one out strategy, we perform random distributed mutations on a sequence. We show that
+\texttt{RNApyro} reconstructs the original sequence with an excellent accuracy.
-
-To benchmark our technique we use the 5S ribosomal RNA family,
- which is around $120$ nucleotides longs. We show
+The pseudo-energetic model and the algorithm is presented in Sec.~\ref{sec:methods}.
+Details of the implementation and benchmarks are in Sec.~\ref{sec:results}.
+Future applications and a discussion are developed in Sec.~\ref{sec:conclusion}.
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@@ -52,7 +52,7 @@
\newcommand{\ub}{\bullet}
%\title{An inside-outside algorithms for mutant RNAs with applications to error detections in structured RNAs}
-\title{An linear inside-outside algorithm for detecting next generation sequencing errors in structured RNAs}
+\title{A linear inside-outside algorithm for detecting next generation sequencing errors in structured RNAs}
\author{}
\date{}

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