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# skbio.alignment.pair_align_nucl

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

  Align two nucleotide sequences.

  This is a convenience wrapper of `pair_align` for nucleotide sequence alignment. It is preloaded with a scoring scheme consistent with BLASTN’s defaults [1]: match score = 2, mismatch score = -3, gap opening penalty = 5, gap extension penalty = 2. All parameters remain customizable. Refer to `pair_align` for full documentation.

  See also

  `pair_align`
  `pair_align_prot`

  References

  [1]

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

  Examples

      >>> from skbio.sequence import DNA
      >>> from skbio.alignment import pair_align_nucl
      >>> seq1 = DNA('GATCGTC')
      >>> seq2 = DNA('ATCGCTC')
      >>> res = pair_align_nucl(seq1, seq2)
      >>> res.score
      5.0

      >>> res.paths[0]
      <PairAlignPath, positions: 8, segments: 4, CIGAR: '1D4M1I2M'>

      >>> res.paths[0].to_aligned((seq1, seq2))
      ['GATCG-TC', '-ATCGCTC']