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.

(Revised version following Martin's suggestion)

\documentclass{article}
\usepackage{xcolor}
\begingroup
\catcode`A\active
\catcode`T\active
\catcode`C\active
\catcode`G\active
\gdef A{\textcolor{red}{\string A}}
\gdef T{\textcolor{green}{\string T}}
\gdef C{\textcolor{blue}{\string C}}
\gdef G{\textcolor{black}{\string G}}
\endgroup

\DeclareRobustCommand\DNA[1]{\begingroup
  \scantokens{%
    \catcode`A\active
    \catcode`C\active
    \catcode`G\active
    \catcode`T\active
    \ttfamily#1\endinput}%
  \endgroup}

\begin{document}

\section{\DNA{ACGT}}

\DNA{ACGTACGT}, \fbox{\DNA{ACGTACGT}}

\end{document}

---

A more professional choice is to use texshade package, especially for biology. I almost forgot it. It is quite complex for me, and there're some predefined styles. You'd better read the manual first.

\begingroup\lccode`~=`A
\lowercase{\endgroup\def~}{\textcolor{red}{A}}
\begingroup\lccode`~=`T
\lowercase{\endgroup\def~}{\textcolor{green}{T}}

\begingroup\lccode`~=`C
\lowercase{\endgroup\def~}{\textcolor{blue}{C}}

\begingroup\lccode`~=`G
\lowercase{\endgroup\def~}{\textcolor{black}{G}}

\let\NX\noexpand
\def\DNAmathcodes{%
  \catcode`A=\active \catcode`T=\active
  \catcode`C=\active \catcode`G=\active
  \catcode`a=\active \catcode`t=\active
  \catcode`c=\active \catcode`g=\active
}

\DeclareRobustCommand{\DNA}{\bgroup\DNAmathcodes\doDNA}
\newcommand\doDNA[1]{\texttt{\uppercase{\scantokens{#1\NX}}}\egroup}


\begin{tabular}{ll}
1 & \DNA{GCATCCAATGCC}\\
2 & \DNA{GGGACCAATGCG}\\
3 & \DNA{TTATCCAATCTC}
\end{tabular}

Note: without \noexpand, \scantokens would add a space; but \noexpand contains an "a"! Also \DNA must be robustified, if we need it in a section title.