skbio.alignment.local_pairwise_align

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 : IUPACSequence

The first unaligned sequence.

seq2 : IUPACSequence

The second unaligned sequence.

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).
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_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 [R102]. The scikit-bio implementation was validated against the EMBOSS water web server [R103].

References

[R102](1, 2) Identification of common molecular subsequences. Smith TF, Waterman MS. J Mol Biol. 1981 Mar 25;147(1):195-7.
[R103](1, 2) http://www.ebi.ac.uk/Tools/psa/emboss_water/