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: |
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Returns: |
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Return type: | tuple |
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 [1]. The scikit-bio implementation was validated against the EMBOSS water web server [2].
References
[1] | Identification of common molecular subsequences. Smith TF, Waterman MS. J Mol Biol. 1981 Mar 25;147(1):195-7. |
[2] | http://www.ebi.ac.uk/Tools/psa/emboss_water/ |