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# skbio.alignment.global_pairwise_align_nucleotide

skbio.alignment.global_pairwise_align_nucleotide(seq1, seq2, gap_open_penalty=5, gap_extend_penalty=2, match_score=1, mismatch_score=-2, substitution_matrix=None, penalize_terminal_gaps=False)

  Globally align nucleotide seqs or alignments with Needleman-Wunsch.

  Parameters:
    seq1 DNA, RNA, or TabularMSA[DNA|RNA]

      The first unaligned sequence(s).

    seq2 DNA, RNA, or TabularMSA[DNA|RNA]

      The second unaligned sequence(s).

    gap_open_penalty int or float, optional

      Penalty for opening a gap (this is subtracted from previous best alignment score, so is typically positive).

    gap_extend_penalty int or float, optional

      Penalty for extending a gap (this is subtracted from previous best alignment score, so is typically positive).

    match_score int or float, optional

      The score to add for a match between a pair of bases (this is added to the previous best alignment score, so is typically positive).

    mismatch_score int or float, optional

      The score to add for a mismatch between a pair of bases (this is added to the previous best alignment score, so is typically negative).

    substitution_matrix: 2D dict (or similar)

      Lookup for substitution scores (these values are added to the previous best alignment score). If provided, this overrides `match_score` and `mismatch_score`.

    penalize_terminal_gaps: bool, optional

      If True, will continue to penalize gaps even after one sequence has been aligned through its end. This behavior is true Needleman-Wunsch alignment, but results in (biologically irrelevant) artifacts when the sequences being aligned are of different length. This is `False` by default, which is very likely to be the behavior you want in all or nearly all cases.

  Returns:
    tuple

      `TabularMSA` object containing the aligned sequences, alignment score (float), and start/end positions of each input sequence (iterable of two-item tuples). Note that start/end positions are indexes into the unaligned sequences.

  See also

  `local_pairwise_align`
  `local_pairwise_align_protein`
  `local_pairwise_align_nucleotide`
  `global_pairwise_align`
  `global_pairwise_align_protein`

  Notes

  Default `match_score`, `mismatch_score`, `gap_open_penalty` and `gap_extend_penalty` parameters are derived from the NCBI BLAST Server [1].

  This function can be use to align either a pair of sequences, a pair of alignments, or a sequence and an alignment.

  References

  [1]

  http://blast.ncbi.nlm.nih.gov/Blast.cgi