folded tetra sequences (len5)

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[5-tile codes of folded tetrahedron sequences (Code length 5)]

The following table shows the frequency of occurrences of 5-tile codes in all the folded tetrahedron sequences
(of length 15 in the case of code width 3 and length 25 in the case of code width 5).
Folded tetrahedron sequences are genarated by program TetraSeqGen as follows:

Folded tetrahedron sequence with "code width 3": TetraSeqGen -w 3 filename.tsg
Folded tetrahedron sequence with "code width 5": TetraSeqGen -w 5 filename.tsg

In particular, "translation" is allowed during the folding process. And two tetrahedron types, 0[xzy] and 0[zxy], are considered as the initial tetrahedron for each U/D-valued sequence. That is, two folded tetrahedron sequences are computed for each U/D sequence.

Remarks:

U/D-valued sequences with "code width 3": DDX-XXX-XXX-XXX-XDD, where X = U or D
U/D-valued sequences with "code width 5": DDDXX-XXXXX-XXXXX-XXXXX-XXDDD, where X = U or D
#{initial tetra type} * #{U/D-sequences} folded tetrahedron sequences are encoded: 2 * 2048 = 4096 in the case of width 3 and 2 * 524288 = 1048576 in the case of width 5.
The ASTRAL column shows the frequency of occurrences of 5-tile codes in the ASTRAL SCOP 1.71 (95%) protein sequence dataset.
"U.A." in the 5-tile code field means "TetraSeqGen could Not Assign any 5-tile code to the fragment."
Click on thumbnail for larger images.

NOTE: Firstly, ("protein backbone") fragments of length five are generated by program TetraSeqGen. Then, each fragment is encoded into the 5-tile code sequence by program ProteinEncoder. In the case of code width 3 (or 5), one should feed TetraSeqGen a binary sequence of length 15 (or 25). (Added on 2011/12/12)