Figure 3

Example illustrating the cost of various dynamic programming algorithms. A typical alignment matrix to illustrating the magnitude of possible savings in computational cost by using a chain-guided alignment in comparison to standard banded dynamic programming. The figure shows the dynamic programming matrix for the semi-global alignment of a reference genome (rows) against a read (columns). The piecewise linear line represents the trace of an optimal alignment. Black parts of this line indicate locations of the seeds forming the chain. Red dots indicate mismatches in the alignment and green lines were not covered by seeds. The band size for banded dynamic programming is indicated in green and the areas in grey indicate the areas in which dynamic programming is performed for a chain-guided alignment. For this example, if banded alignment saves 86% of the matrix, chain-guided alignment saves 88% of the banded matrix.