Figure 1: An example to show the tree structure of k-mer counting. | Scientific Reports

Figure 1: An example to show the tree structure of k-mer counting.

From: Recombination spot identification Based on gapped k-mers

Figure 1

This example only contains two alphabets, A and T. We use k = 3 and three sequences S1 = AAAAT, S2 = ATTTT, and S3 = AATA to build k-mer tree. Each node ti at depth d represents a sequence of length d, denoted by s(ti), which is determined by the path from the root of the tree to ti. At depth d = 3, for node t6, s(t6) = ‘AAA’, S1 contains two counts of this k-mer, S2 and S3 do not contain this k-mer. For node t7, s(t7) = ‘AAT’, S1 and S3 both contain one count, and S2 does not contain this k-mer. Compared t6 with t7, the paths to these two nodes only contain one mismatch.

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