Commit de2695e1 authored by Vladimir Reinharz's avatar Vladimir Reinharz
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Figure 4 and 7 redone

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TeX/NAR/Figure4.png

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...@@ -435,12 +435,14 @@ The adenine riboswitch RF00167 ...@@ -435,12 +435,14 @@ The adenine riboswitch RF00167
} }
\begin{figure}[ht!] \begin{figure*}[ht!]
\centering \centering
\includegraphics[width=0.47\textwidth]{Figure4.png} \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 $\Delta(S, S_i)$.} \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 $\Delta(S, S_i)$.}
\label{fig:shape} \label{fig:shape}
\end{figure} \end{figure*}
We also built a secondary test set of \rfam families with experimentally determined 3D structures. 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. We also built a secondary test set of \rfam families with experimentally determined 3D structures. 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.
...@@ -526,12 +528,14 @@ structural differences. We present in Fig.~\ref{fig:dist} the distribution of pa ...@@ -526,12 +528,14 @@ structural differences. We present in Fig.~\ref{fig:dist} the distribution of pa
\begin{figure}[ht!] \begin{figure*}[ht!]
\centering \centering
\includegraphics[width=0.47\textwidth]{Figure7.png} \colorbox{red}{
\includegraphics[width=0.96\textwidth]{Figure7.png}
}
\caption{{\bf Distance distribution for pairs of secondary structure elements}, weighted by the numbers of non-shared nucleotides} \caption{{\bf Distance distribution for pairs of secondary structure elements}, weighted by the numbers of non-shared nucleotides}
\label{fig:dist} \label{fig:dist}
\end{figure} \end{figure*}
...@@ -581,7 +585,7 @@ The poorest results are achieved in family RF01118. Interestingly, one of the co ...@@ -581,7 +585,7 @@ The poorest results are achieved in family RF01118. Interestingly, one of the co
\begin{figure*}[ht!] \begin{figure*}[ht!]
\centering \centering
\includegraphics[width=\textwidth]{Figure9.png} \includegraphics[width=0.96\textwidth]{Figure9.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 \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}.} 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} \label{fig:rfam_best_bit}
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