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\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{Bio} \PYG{k+kn}{import} \PYG{n}{Align}
\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.Align} \PYG{k+kn}{import} \PYG{n}{substitution\PYGZus{}matrices}
\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}{aligner} \PYG{o}{=} \PYG{n}{Align}\PYG{o}{.}\PYG{n}{PairwiseAligner}\PYG{p}{()}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{open\PYGZus{}gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{10}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{extend\PYGZus{}gap\PYGZus{}score} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mf}{0.5}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{aligner}\PYG{o}{.}\PYG{n}{substitution\PYGZus{}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{n}{score} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{score}\PYG{p}{(}\PYG{n}{seq1}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{,} \PYG{n}{seq2}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{score}\PYG{p}{)}
\PYG{g+go}{292.5}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{alignments} \PYG{o}{=} \PYG{n}{aligner}\PYG{o}{.}\PYG{n}{align}\PYG{p}{(}\PYG{n}{seq1}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{,} \PYG{n}{seq2}\PYG{o}{.}\PYG{n}{seq}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{)}
\PYG{g+go}{2}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{o}{.}\PYG{n}{score}\PYG{p}{)}
\PYG{g+go}{292.5}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{alignments}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{])}  \PYG{c+c1}{\PYGZsh{}doctest: +ELLIPSIS}
\PYG{g+go}{MV\PYGZhy{}LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF\PYGZhy{}DLS\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}HGSAQVKGHGKKV...}
\PYG{g+go}{||\PYGZhy{}|.|..|..|.|.||||\PYGZhy{}\PYGZhy{}...|.|.|||.|.....|.|...|..|\PYGZhy{}|||\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}.|...||.|||||...}
\PYG{g+go}{MVHLTPEEKSAVTALWGKV\PYGZhy{}\PYGZhy{}NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKV...}
\PYG{g+go}{\PYGZlt{}BLANKLINE\PYGZgt{}}
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