\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.Align} \PYG{k+kn}{import} \PYG{n}{substitution\PYGZus{}matrices}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{substitution\PYGZus{}matrices}\PYG{o}{.}\PYG{n}{load}\PYG{p}{()}  \PYG{c+c1}{\PYGZsh{}doctest: +ELLIPSIS}
\PYG{g+go}{[\PYGZsq{}BENNER22\PYGZsq{}, \PYGZsq{}BENNER6\PYGZsq{}, \PYGZsq{}BENNER74\PYGZsq{}, \PYGZsq{}BLOSUM45\PYGZsq{}, \PYGZsq{}BLOSUM50\PYGZsq{}, \PYGZsq{}BLOSUM62\PYGZsq{}, ..., \PYGZsq{}STR\PYGZsq{}]}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{matrix} \PYG{o}{=} \PYG{n}{substitution\PYGZus{}matrices}\PYG{o}{.}\PYG{n}{load}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}BLOSUM62\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k}{print}\PYG{p}{(}\PYG{n}{matrix}\PYG{p}{)}  \PYG{c+c1}{\PYGZsh{}doctest: +ELLIPSIS}
\PYG{g+go}{\PYGZsh{}  Matrix made by matblas from blosum62.iij}
\PYG{g+gp}{...}
\PYG{g+go}{     A    R    N    D    C    Q ...}
\PYG{g+go}{A  4.0 \PYGZhy{}1.0 \PYGZhy{}2.0 \PYGZhy{}2.0  0.0 \PYGZhy{}1.0 ...}
\PYG{g+go}{R \PYGZhy{}1.0  5.0  0.0 \PYGZhy{}2.0 \PYGZhy{}3.0  1.0 ...}
\PYG{g+go}{N \PYGZhy{}2.0  0.0  6.0  1.0 \PYGZhy{}3.0  0.0 ...}
\PYG{g+go}{D \PYGZhy{}2.0 \PYGZhy{}2.0  1.0  6.0 \PYGZhy{}3.0  0.0 ...}
\PYG{g+go}{C  0.0 \PYGZhy{}3.0 \PYGZhy{}3.0 \PYGZhy{}3.0  9.0 \PYGZhy{}3.0 ...}
\PYG{g+go}{Q \PYGZhy{}1.0  1.0  0.0  0.0 \PYGZhy{}3.0  5.0 ...}
\PYG{g+gp}{...}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{substitution\PYGZus{}matrix} \PYG{o}{=} \PYG{n}{matrix}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{score} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}ACDQ\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}ACDQ\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{score}
\PYG{g+go}{24.0}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{score} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}ACDQ\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}ACNQ\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{score}
\PYG{g+go}{19.0}
\end{Verbatim}
