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# skbio.alignment.pair_align_prot

skbio.alignment.pair_align_prot(seq1, seq2, /, **kwargs)

  Align two protein sequences.

  This is a convenience wrapper of `pair_align` for protein sequence alignment. It is preloaded with a scoring scheme consistent with BLASTP’s defaults [1]: substitution matrix = BLOSUM62, gap opening penalty = 11, gap extension penalty = 1. All parameters remain customizable. Refer to `pair_align` for full documentation.

  See also

  `pair_align`
  `pair_align_nucl`

  References

  [1]

  https://www.ncbi.nlm.nih.gov/books/NBK279684/

  Examples

      >>> from skbio.sequence import Protein
      >>> from skbio.alignment import pair_align_prot
      >>> seq1 = Protein('PKKKRKV')
      >>> seq2 = Protein('PAAKRVKLD')
      >>> res = pair_align_prot(seq1, seq2)
      >>> res.score
      11.0

      >>> res.paths[0]
      <PairAlignPath, positions: 9, segments: 2, CIGAR: '7M2I'>

      >>> res.paths[0].to_aligned((seq1, seq2))
      ['PKKKRKV--', 'PAAKRVKLD']