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.

multiple-alignment.pdf

multiple-alignment.png

multiple-alignment.tex

\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}