skbio.alignment.
local_pairwise_align
(seq1, seq2, gap_open_penalty, gap_extend_penalty, substitution_matrix)[source]¶Locally align exactly two seqs with Smith-Waterman
State: Experimental as of 0.4.0.
Parameters: | seq1 : GrammaredSequence
seq2 : GrammaredSequence
gap_open_penalty : int or float
gap_extend_penalty : int or float
substitution_matrix: 2D dict (or similar)
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Returns: | tuple
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See also
local_pairwise_align_protein
, local_pairwise_align_nucleotide
, skbio.alignment.local_pairwise_align_ssw
, global_pairwise_align
, global_pairwise_align_protein
, global_pairwise_align_nucelotide
Notes
This algorithm was originally described in [R106]. The scikit-bio implementation was validated against the EMBOSS water web server [R107].
References
[R106] | (1, 2) Identification of common molecular subsequences. Smith TF, Waterman MS. J Mol Biol. 1981 Mar 25;147(1):195-7. |
[R107] | (1, 2) http://www.ebi.ac.uk/Tools/psa/emboss_water/ |