8 * Created by Pat Schloss on 12/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
13 * Gotoh O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162:705-8.
14 * Myers, EW & Miller, W. 1988. Optimal alignments in linear space. Comput Appl Biosci. 4:11-7.
16 * This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
17 * in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
18 * Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
19 * method to fix the ends (see Overlap class documentation)
24 #include "alignment.hpp"
26 /**************************************************************************************************/
28 class GotohOverlap : public Alignment {
31 GotohOverlap(float, float, float, float, int);
32 void align(string, string);
43 /**************************************************************************************************/