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Fig. 3 | Algorithms for Molecular Biology

Fig. 3

From: Bi-alignments with affine gaps costs

Fig. 3

Shifts in a bi-alignment. The bi-alignment consists of two alignments \(\mathbb {U}\) or \(\mathbb {V}\) (colored horizontal boxes) of the pair of objects \(\mathbf {a}\) and \(\mathbf {b}\) that are aligned with each other two different ways i.e. w.r.t. to two different objective functions. Since the actual letters in \(\mathbf {a}\) and \(\mathbf {b}\) are irrelevant for definition of shifts, we distinguish only letters (filled circles) and gaps (dashes). Note that \(\mathbf {a}\) and \(\mathbf {b}\) may be represented by different alphabets in \(\mathbf {U}\) and \(\mathbf {V}\). Insertions and deletions in the alignment of alignments \(\mathbb {W}\), i.e. the alignment of the columns of \(\mathbb {U}\) with the columns of \(\mathbb {W}\), are (highlighted by darker colors) correspond to all-gap columns in either \(\mathbb {U}\) or \(\mathbb {V}\). Aligned columns in \(\mathbb {W}\) are shifts if the gap patterns in the upper pair and the lower pair differ. Colored outlines distinguish single (blue) and double shifts (red)

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