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.
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
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.