Secondary structure of a toy ncRNA sequence. A small example for vector graphics programming in LaTeX using the tikz package.

secondary-structure.pdf

secondary-structure.png

secondary-structure.tex

\documentclass{standalone} % Package 'standalone' allows to compile tikz images independently or to incorporate them into LaTeX documents
\usepackage{tikz}
\usetikzlibrary{matrix}
\begin{document}
\begin{tikzpicture}
[nucl/.style={black, circle, draw=black, fill=black!10, minimum size=2em},
A/.style={nucl, fill=red!30},
G/.style={nucl, fill=blue!30},
C/.style={nucl, fill=green!30},
U/.style={nucl, fill=yellow!30},
molEnd/.style={fill=none, draw=none, minimum size=2em}]
% Secondary strcuture
\matrix (m2) [matrix of nodes, row sep=1.5em, column sep=1.5em, nodes=nucl, ampersand replacement=\&] {
% 1                2           3           4        5           6         7         8
                \&         \&         \&         \&         \& |[C]| C \& |[C]| C \&         \\ % 1
|[molEnd]| {5'} \& |[U]| U \& |[G]| G \& |[G]| G \& |[A]| A \&         \&         \& |[C]| C \\ % 2
|[molEnd]| {3'} \& |[A]| A \& |[C]| C \& |[C]| C \& |[U]| U \&         \&         \& |[A]| A \\ % 3
                \&         \&          \&        \&         \& |[U]| U \& |[U]| U \&         \\ % 4
};
% Backbone
\path
(m2-2-1) edge (m2-2-2)
(m2-2-2) edge (m2-2-3)
(m2-2-3) edge (m2-2-4)
(m2-2-4) edge (m2-2-5)
(m2-2-5) edge (m2-1-6)
(m2-1-6) edge (m2-1-7)
(m2-1-7) edge (m2-2-8)
(m2-2-8) edge (m2-3-8)
(m2-3-8) edge (m2-4-7)
(m2-4-7) edge (m2-4-6)
(m2-4-6) edge (m2-3-5)
(m2-3-5) edge (m2-3-4)
(m2-3-4) edge (m2-3-3)
(m2-3-3) edge (m2-3-2)
(m2-3-2) edge (m2-3-1);
% Basepairs
\path
(m2-2-2) edge (m2-3-2)
(m2-2-3) edge (m2-3-3)
(m2-2-4) edge (m2-3-4)
(m2-2-5) edge (m2-3-5);
\end{tikzpicture}
\end{document}