[Structural alignment    (Basic ideas)]

(1) Structural alignment

We could use 5-tile code sequences to align polygonal chains.

As an example, let's consider alignment of the three polygonal chains of different lengths in figure A.
As you see, the 5-tile code sequence of the black and the red chains are 78% identical, the 5-tile code sequence of the black and the blue chains are 75% identical, and the 5-tile code sequence of the red and the blue chains are 60% identical.

Superimpositions of the chains shown below confirm the correspondence between the 5-tile code sequence similarity and structural similarity.

In this case, we could say the black chain is more similar to the red one than to the blue one.

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Fig. A: Sequence similarity and structural similarity

(2) Multiple-alignment and structural blocks

Since the 5-tile code is encoding local structures, we could extract common structural blocks among multiple polygonal chains by aligning them at once.

For example, if we align the three polygonal chains given above, we antomatically obtain three structural blocks which compose the polygonal chains. Their 5-tile code sequences are 9H, IA, and 81 respectively as shown on the right.

Note that it is not trivial to detect the second common block of 5-tile code sequence IA.

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Fig. B: Extraction of common structural blocks