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Fig. 8 | Genome Biology

Fig. 8

From: GraphAligner: rapid and versatile sequence-to-graph alignment

Fig. 8

Left: regular banded alignment with b=3. The reference is on top and the query on the left. The gray cells are inside the band and are calculated. The blue line shows the traceback of the optimal alignment. Right: score based banding with b=1. The reference is on top and the query on the left. The gray cells are inside the band and the blue line is the traceback. The red-circled cells are the minimum for each row, which are discovered during the calculation of the matrix and define whether a cell is inside the band or not; a cell is inside the band if its score is within b of the minimum score in the same row. The cells with a number on a white background are calculated to discover the end of the band, but they are not inside the band and are ignored when calculating the next row. The band can wander around the DP matrix and change size, automatically spreading wider in high error areas and narrower in low error areas. Note that the score-based banding parameter is 1 in comparison to 3 in the regular banding to the left. The implementation uses a coarser band of 64 x 64 blocks instead of individual cells

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