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Sequence-structure alignment of a toy data set consisting of four homologous ncRNA sequences and their joint secondary structure. A small example for vector graphics programming in LaTeX using the tikz package.
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\documentclass{standalone} % Package 'standalone' allows to compile tikz images independently or to incorporate them into LaTeX documents | |
\usepackage{tikz} | |
\usetikzlibrary{matrix} | |
\pgfdeclarelayer{background} | |
\pgfsetlayers{background,main} | |
\begin{document} | |
\begin{tikzpicture} | |
[cons/.style={rounded corners}, | |
high-cons/.style={cons, draw=red, fill=red!20}, | |
mid-cons/.style={cons, draw=orange, fill=orange!20}, | |
low-cons/.style={cons, draw=green, fill=green!20}] | |
% Sequence alignment as a matrix of nodes | |
\matrix (s) [matrix of nodes, row sep=.05em, column sep=.2em, ampersand replacement=\&] { | |
% 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | |
human \& \& U \& C \& G \& U \& C \& C \& C \& U \& U \& U \& U \& C \& G \& A \\% 1 | |
chicken \& \& U \& G \& G \& A \& C \& C \& C \& A \& U \& U \& U \& C \& C \& A \\ % 2 | |
mouse \& \& U \& C \& C \& A \& C \& C \& C \& - \& U \& U \& U \& G \& G \& A \\ % 3 | |
pig \& \& U \& A \& C \& A \& C \& C \& - \& U \& U \& U \& U \& G \& U \& A \\ % 4 | |
sec. structure \& \& ( \& ( \& ( \& ( \& . \& . \& . \& . \& . \& . \& ) \& ) \& ) \& ) \\ % 5 | |
}; | |
% Highlight conserved base pairs in different colors | |
\begin{pgfonlayer}{background} | |
% Opening brackets | |
\fill[high-cons] (s-1-3.north west) rectangle (s-4-3.south east); | |
\fill[low-cons] (s-1-4.north west) rectangle (s-4-4.south east); | |
\fill[mid-cons] (s-1-5.north west) rectangle (s-4-5.south east); | |
\fill[high-cons] (s-2-6.north west) rectangle (s-4-6.south east); | |
% Closing brackets | |
\fill[high-cons] (s-2-13.north west) rectangle (s-4-13.south east); | |
\fill[mid-cons] (s-1-14.north west) rectangle (s-4-14.south east); | |
\fill[low-cons] (s-1-15.north west) rectangle (s-4-15.south east); | |
\fill[high-cons] (s-1-16.north west) rectangle (s-4-16.south east); | |
\end{pgfonlayer} | |
\end{tikzpicture} | |
\end{document} |
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