Figure 1
From: DNACLUST: accurate and efficient clustering of phylogenetic marker genes
Dynamic programming table example. Partially filled dynamic programming table. The query sequence is represented on the horizontal axis. At this point the algorithm has computed the alignment costs for a prefix of length 4 of the data sequences - which is shown on the vertical axis. Since we are calculating semi-global alignment the first row is initialized to all zeroes, i.e. The alignment of the shorter data sequence can start at any position of the longer query sequence without any penalty. In this figure, the distance threshold is 2, and any values larger than this threshold are set to the maximum value represented by ∞. To optimize the running time, since there are only three valid values on the last finished row, only the values for the three gray cells need to be computed on row right above it.