align_pairwise(sequence1,
sequence2,
algorithm='NW70',
matrix='BLOSUM62',
gap_open_penalty=1.0,
gap_extend_penalty=1.0,
end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0,
verbosity=1)
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Align two protein sequences.
- Parameters:
sequence1 (str) - The first protein sequence as one letter codes.sequence2 (str) - The second protein sequence as one letter codes.algorithm (str) - The pairwise sequence alignment algorithm to use.matrix (str) - The substitution matrix to use.gap_open_penalty (float) - The penalty for introducing gaps, as a positive number.gap_extend_penalty (float) - The penalty for extending a gap, as a positive number.end_gap_open_penalty (float) - The optional penalty for opening a gap at the end of a sequence.end_gap_extend_penalty (float) - The optional penalty for extending a gap at the end of a
sequence.verbosity (int) - The level of verbosity. Setting this to zero silences all
printouts. - Returns: float, str, str, numpy rank-2 int array
- The alignment score, two alignment strings and the gap matrix.
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