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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