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 : GrammaredSequence

The first unaligned sequence.

seq2 : GrammaredSequence

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.

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/