Aligner

This module implements the aligner.

class Data(score: float)

Private data class for the Needleman-Wunsch+Gotoh sequence aligner.

__init__(score: float)

score: float: The current score.

p: float: \(P_{m,n}\) in [Gotoh1982].

q: float: \(Q_{m,n}\) in [Gotoh1982].

pSize: int: The size of the p gap. \(k\) in [Gotoh1982].

qSize: int: The size of the q gap. \(k\) in [Gotoh1982].

class Aligner(start_score: float = - 1.0, open_score: float = - 1.0, extend_score: float = - 0.5)

A generic Needleman-Wunsch+Gotoh sequence aligner.

This implementation uses Gotoh’s improvements to get \(\mathcal{O}(mn)\) running time and reduce memory requirements to essentially the backtracking matrix only. In Gotoh’s technique the gap weight formula must be of the special form \(w_k = uk + v\) (affine gap). \(k\) is the gap size, \(v\) is the gap opening score and \(u\) the gap extension score.

The aligner is type-agnostic and expects only to call the method Strategy.similarity() on the given strategy.