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# skbio.alignment.global_pairwise_align

`skbio.alignment.``global_pairwise_align`(seq1, seq2, gap_open_penalty, gap_extend_penalty, substitution_matrix, penalize_terminal_gaps=False)

  Globally align a pair of seqs or alignments with Needleman-Wunsch

  State: Experimental as of 0.4.0.

  Parameters:

  - seq1 (GrammaredSequence or TabularMSA) – The first unaligned sequence(s).
  - seq2 (GrammaredSequence or TabularMSA) – The second unaligned sequence(s).
  - gap_open_penalty (int or float) – Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).
  - gap_extend_penalty (int or float) – Penalty for extending a gap (this is substracted from previous best alignment score, so is typically positive).
  - substitution_matrix (2D dict (or similar)) – Lookup for substitution scores (these values are added to the previous best alignment 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: | `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.
  Return type: | tuple

  See also

  `local_pairwise_align()`, `local_pairwise_align_protein()`, `local_pairwise_align_nucleotide()`, `skbio.alignment.local_pairwise_align_ssw()`, `global_pairwise_align_protein()`, `global_pairwise_align_nucelotide()`

  Notes

  This algorithm (in a slightly more basic form) was originally described in [1]. The scikit-bio implementation was validated against the EMBOSS needle web server [2].

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

  References

  [1] | A general method applicable to the search for similarities in the amino acid sequence of two proteins. Needleman SB, Wunsch CD. J Mol Biol. 1970 Mar;48(3):443-53.

  [2] | http://www.ebi.ac.uk/Tools/psa/emboss_needle/