Commit 174e550b authored by Vladimir Reinharz's avatar Vladimir Reinharz
Browse files

moved all figs to correct number, fixed main accordingly

parent c58921fa
TeX/NAR/Figure4.png

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......@@ -424,19 +424,10 @@ The MaM cobalamin riboswitch sequence can be found in the \rfam family \texttt{R
The adenine riboswitch belongs to family \texttt{RF00167} which has $133$ seed sequences. The structure with the adenine ligand�has PDB identifier \texttt {1Y26}. Three different MaM experiments were conducted on this molecule. Experiments \texttt{Adenine\char`_2} and \texttt{Adenine\char`_3} where done in presence of the ligand, and are used in this paper. The third experiment \texttt{Adenine\char`_4} has been performed in absence of the ligand, and thus was omitted from this benchmark since disruptive mutations cannot be used to detect key structural elements of the ligand-bound structure. Nonetheless, the results are indicated in the supplementary material.
%Fig.~\ref{fig:shape} shows for every molecule and position $i$, the disruption of the shape profile when a mutation occurs at that position (i.e. $\Delta(S, S_i)$). We also display the \rfam consensus secondary structure at the bottom. We notice the rugged landscape and the sharp differences between the adenine riboswitch profile 4, where the MaM was done without the presence of adenine, and the other two. Additionally, the fact that the glycosine riboswitch sequence is mostly aligned to non structured part might be an additional reason for the poor results of our method.
}
%\begin{figure*}[ht!]
% \centering
% \colorbox{red}{
% \includegraphics[width=0.96\textwidth]{Figure4.png}
% }
% \caption{{\bf Disruptive impact of mutations, as measured from MaM data.} On the $x$-axis the position of the mutation, and on the $y$-axis the value of the SHAPE profile distance $\Delta(S, S_i)$. {\color{red} The adenine\_4 MaM experiment was done in the absence of adenine.}}
% \label{fig:shape}
%\end{figure*}
{\color{red} To complete our benchmark, we also built a secondary test set of \rfam families with experimentally determined 3D structures, but for which MaM experiments were not available.} We selected all \rfam families with sequences having a size ranging from 35 to 150 nucleotides, and with PDB files containing at least one other molecule in the vicinity of the RNA. In total, we found 14 families matching 729 different structures.
......@@ -474,14 +465,14 @@ We evaluated \soft on a comprehensive set of values for $\delta$ the \shape pro
\centering
\colorbox{red}{
\begin{subfigure}{\textwidth}
\includegraphics[width=0.96\textwidth]{Figure5.png}
\includegraphics[width=0.96\textwidth]{Figure4.png}
\caption{MaM}
\label{fig:auc}
\end{subfigure}
}
\colorbox{red}{
\begin{subfigure}{\textwidth}
\includegraphics[width=0.96\textwidth]{Figure5b.png}
\includegraphics[width=0.96\textwidth]{Figure4b.png}
\caption{\remu}
\label{fig:auc_remu}
\end{subfigure}
......@@ -529,7 +520,7 @@ We conjecture that the differences in the influence of the $\gamma$ parameter, m
\begin{figure}[th!]
\centering
\colorbox{red}{
\includegraphics[width=0.47\textwidth]{Figure6.png}
\includegraphics[width=0.47\textwidth]{Figure5.png}
}
\caption{{\bf Distance distribution for pairs of secondary structure elements}, weighted by the numbers of non-shared nucleotides. {\color{red} The different distribution affect the quantity
of positions selected by the parameter $\gamma$, distance from the mutation.}}
......@@ -547,7 +538,7 @@ by compensating the effect of a disruptive mutation.
\begin{figure}[ht!]
\centering
\includegraphics[width=0.47\textwidth]{Figure7.png}
\includegraphics[width=0.47\textwidth]{Figure6.png}
\caption{{\bf Predicted positions and interacting chains of the 5S rRNA \texttt{3OFC} structure.} In red on the top right behind purple spheres is the disrupting mutation, in green the predicted position with high mutual information. The spheres around the RNA represent the subset of nucleotides at most at \SI{5}{\angstrom} from the rRNA, from other chains in the complex. The other spheres belong to other molecules. Each sphere is color-coded to indicate its chain as follows. Chain A is black, Z purple, W pink, V light blue, O beige, F yellow and M orange.}
\label{fig:5s_3d}
\end{figure}
......@@ -578,7 +569,7 @@ The poorest results are achieved in family RF01118. Interestingly, one of the co
\begin{figure*}[t!]
\centering
\includegraphics[width=0.96\textwidth]{Figure8.png}
\includegraphics[width=0.96\textwidth]{Figure7.png}
\caption{ {\bf Performance of \soft for \remu-predicted disruptions.} For each \rfam family, we consider all PDBs having less than 150 nucleotides, and having maximal matching score to family. For a set of extreme percentile cutoff of the \shape profile disruption in the first column (computational \remu disruption in the second
column) $\delta$ and a minimal distance $\gamma$ from the mutation. Note that the PDB models considered for the 5S family (RF0001) do not match those investigated by MaM, which explains the discrepancies observed between the results above and those of Fig.~\ref{fig:aucremumam}.\label{fig:rfam_best_bit}}
\end{figure*}
......
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