\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio} \PYG{k+kn}{import} \PYG{n}{pairwise2}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio} \PYG{k+kn}{import} \PYG{n}{SeqIO}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio.SubsMat.MatrixInfo} \PYG{k+kn}{import} \PYG{n}{blosum62}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{seq1} \PYG{o}{=} \PYG{n}{SeqIO}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}alpha.faa\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}fasta\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{seq2} \PYG{o}{=} \PYG{n}{SeqIO}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{l+s+s2}{\PYGZdq{}beta.faa\PYGZdq{}}\PYG{p}{,} \PYG{l+s+s2}{\PYGZdq{}fasta\PYGZdq{}}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{alignments} \PYG{o}{=} \PYG{n}{pairwise2}\PYG{o}{.}\PYG{n}{align}\PYG{o}{.}\PYG{n}{globalds}\PYG{p}{(}\PYG{n}{seq1}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{,} \PYG{n}{seq2}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{,} \PYG{n}{blosum62}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{10}\PYG{p}{,} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{0.5}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{)}
\PYG{g+go}{2}
\end{Verbatim}
