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Figure 2 | BMC Bioinformatics

Figure 2

From: Topological characterization of neuronal arbor morphology via sequence representation: I - motif analysis

Figure 2

Measuring k-mers. a. Highlighted dimers in a portion of a fly tangential cell [64] and its associated sequence. b. Dimer schematics displaying the possible configurations. Triangles represent subtrees of unspecified size and shape. Bold segments indicate branches leading to the larger side subtree of the parent A node. Given the (Smaller then Larger) traversal method, the TT dimer must be preceded by an A. TA and TC schematics are examples, as additional bifurcations could be found between the parent A and small-side T nodes. c. Number of k-mers (with examples) by k shows an approximately exponential rise. d. Calculating the percentile rank of a k-mer given the distribution of k-mer counts in the source sequence’s surrogate population. An example apical dendrite (NMO_02582 from [65]), dendrogram, and sequence are shown along with cumulative distribution of k-mer counts for k-mers AT (red) and AC (green). Below: Six out of 100 node-type-constrained surrogates are shown. The example k-mers are highlighted and their counts compose the distributions. Colored dots show the respective percentile ranks of the apical dendrite k-mer counts, with AT being above nearly the entire surrogate distribution (thus constituting a motif) and AC being “captured” inside the middle 95% of its surrogate distribution.

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