[Tex/LaTex] Underlining a coloured DNA sequence

colorformattingverbatim

In the posts to the question of Timtico (here) several ways have been proposed to colour the As,Ts,Cs and Gs differently within a DNA sequence. What I want is also to be able to underline some nucleotides to emphasise them, e.g.: \dna{ATACAG$\underbar{AG}$CATA} but I didn't manage to do so.
Does anyone have suggestions to this problem?
Thank you very much!

Best Answer

I added a delimiter to the code from my answer at typesetting different characters with different colors in a DNA sequence

\documentclass{article}
\usepackage{listings,xcolor}
\lstdefinestyle{dna}{%
    literate={A}{\textcolor{green}{A}}{1}
        {B}{\textcolor{blue}{B}}{1}
        {C}{\textcolor{red}{C}}{1}
        {a}{\textcolor{green}{A}}{1}
        {b}{\textcolor{blue}{B}}{1}
        {c}{\textcolor{red}{C}}{1},
    basicstyle=\ttfamily,
    moredelim=[is][\underline]{_}{_}
}
\newcommand{\DNA}[1]{%
    \lstinline[style=dna]{#1}%
}
\begin{document}
\DNA{AA_CAAAD_A}
\end{document}

The result is
result of the above code

I think, this should work for you.

Related Solutions

[Tex/LaTex] typesetting different characters with different colors in a DNA sequence

Like this?

[EDIT: I changed the example so it doesn’t touch other listings.]

\documentclass{article}
\usepackage{listings,xcolor}
\lstdefinestyle{dna}{%
    literate={A}{\textcolor{green}{A}}{1}
        {B}{\textcolor{blue}{B}}{1}
        {C}{\textcolor{red}{C}}{1}
        {a}{\textcolor{green}{A}}{1}
        {b}{\textcolor{blue}{B}}{1}
        {c}{\textcolor{red}{C}}{1},
    basicstyle=\ttfamily,
}
\newcommand{\DNA}[1]{%
    \lstinline[style=dna]{#1}%
}
\begin{document}
\lstinline{ABCabc}\quad\DNA{bbCa}
\section{Somthing about \DNA{abcabcababc}}
\end{document}

You can use it also in commands like \section See the listingsmanual for more info.

[Tex/LaTex] Page border coloured

You could use TikZ

This example can give an idea how to use it:

\documentclass[english]{scrbook}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{babel,blindtext}

\usepackage{scrpage2}
\usepackage{tikz}
\usetikzlibrary{calc}
\newcommand{\pageframe}{%
    \begin{tikzpicture}[remember picture, overlay]
        % page frame
        \fill [red] (current page.north west)
            rectangle (current page.south east);
        \fill [white, rounded corners=1cm] ($(current page.north west)+(1cm,-1cm)$)
                    rectangle ($(current page.south east)+(-1cm,4cm)$);
        \node [fill=green, text width=1.5cm, align=center] at
            ($(current page.south)+(0,4cm)$) {\strut\pagemark};
            % \strut gives all page mark nodes the same hight.
    \end{tikzpicture}
}
% set page style
\cehead[\pageframe]{\pageframe}
\cohead[\pageframe]{\pageframe}
\pagestyle{scrheadings}

\begin{document}
\Blinddocument
\end{document}

When using different definitions of \cehead and \lefoot (or other heading-commads) you can define different borders for left and right pages. You can even “draw” the pagemark with the TikZ way.

Note that TikZ needs two latex-runs to get the right positions.

See PGF Manual, section 16.13.2 Referencing the Current Page Node – Absolute Positioning and the KOMA-Script Manual about using scrpage2.

Best Answer

Related Solutions

[Tex/LaTex] typesetting different characters with different colors in a DNA sequence

[Tex/LaTex] Page border coloured

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