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Figure 1 | BMC Bioinformatics

Figure 1

From: Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment

Figure 1

Pairwise global sequence alignment. a. Changes in tree structure are reflected in sequence representation. When a side-branch is lost from a non-T node or a T-node with a C parent, a C node is removed from the sequence. When a branch is lost from a T node with an A parent, the T is removed and the parent A becomes a C. b. Two tree-derived sequences are aligned by matching characters and placing gaps when an alignment cannot be made. C nodes or entire subtrees are gapped, from an A to its associated T (orange brackets). The A at the front of a gap region can be matched to a C (purple connected bracket). Matches (blue |) count as 1 point, gaps (orange X) count as -1 point, and openings of a gap region count as -3 points. Alignment scores are normalized and converted into distance values. c. Sample apical dendrite morphologies of hippocampal CA1 and CA3 pyramidal cells (NMO_00588, 07558, 00219, 00213) [51-53] and their topology dendrograms illustrate alignments between neurites of the same sub-region along with normalized distances for all 6 pairs. Raw alignment scores are also provided for within-class alignments. Inset: Within- and between-group distributions of normalized distances (with mean ± standard deviation) indicate that the pyramidal apical dendrites are topologically more similar to apical dendrites of their own group than to those in the other group.

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