skbio.alignment.local_pairwise_align

skbio.alignment.local_pairwise_align(seq1, seq2, gap_open_penalty, gap_extend_penalty, substitution_matrix)

Locally align exactly two seqs with Smith-Waterman.

Parameters:

seq1GrammaredSequence

The first unaligned sequence.

seq2GrammaredSequence

The second unaligned sequence.

gap_open_penaltyint or float

Penalty for opening a gap (this is substracted from previous best alignment score, so is typically positive).

gap_extend_penaltyint 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 [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/