[From 2008-01-02 to 2008-12-29]

2008-12-29: Add the "See more ..." section:  (1) Robustness and (2) Sensitivity.
                     See EXAMPLES (Encoding/Decoding) > Statistics.

2008-12-23: Add (4) Flexibility, (5) Code pref., and (6) Freq. dist.. of the "statistics of the D2 code" section.
                     See EXAMPLES (Encoding/Decoding) >  Statistics.
2008-12-22: Add (3) Selectivity of the "statistics of the D2 code" section.
                     See EXAMPLES (Encoding/Decoding) >  Statistics.
2008-12-21: Add (1) Robustness and (2) Sensitivity of the "statistics of the D2 code" section.
                     See EXAMPLES (Encoding/Decoding) >  Statistics.

2008-12-03: Add examples of HIV-1 PR variants (NMR structures / 1BVE (DIMER))
                     See EXAMPLES (Prediction/Alignment/Others) >  Structural alignment > HIV-1 PR variants.

2008-12-01: Add examples of HIV-1 PR variants (space group P61)
                     See EXAMPLES (Prediction/Alignment/Others) >  Structural alignment > HIV-1 PR variants.

2008-11-29: Enable the "nowrap" option in table cells of D2 code and DSSP sequences
                     See EXAMPLES (Prediction/Alignment/Others) >  Structural alignment > Fold change and Multi-struct. sequences.
2008-11-29: Add examples of HIV-1 PR variants
                     See EXAMPLES (Prediction/Alignment/Others) >  Structural alignment.

2008-10-25: Add manuscript of "Systematic analysis of local flexibility of multiple-structure proteins."
                     See PAPERS / Protein structure and RNA aptamer structure.

2008-09-27: Add Mathematical definitions in the Research section (2).

2008-09-14: Add [NOTE] in the Research section (2a).

2008-09-11: Add section (5) Specification of hetero numbers. See the Research page.
2008-09-11: Add examples of surface flow on a discrete manifold. See the Research section (2a).
2008-09-11: Renew the Research page.

2008-08-12: An alias of the 5-tile code is proposed: "D2 code." See the Research section (1).
2008-08-12: Correction in the definition of chameleon sequences: secondary structure ==> "regular" secondary structure.
                     See EXAMPLES (Prediction/Alignment/Others) > Multiple-structure sequences.

2008-07-29: New release, ProteinViewer ver. 0.6.  (support black and white spheres and others)

2008-06-09: Add examples of proteins with short/mid-sized/long variable regions.
                    See EXAMPLES (Prediction/Alignment/Others) > Multiple-structure sequences.
2008-06-08: Add a frequency distribution table for the variable regions of length 1
                    See EXAMPLES (Prediction/Alignment/Others) > Multiple-structure sequences.
2008-06-07: Add Length frequency distribution of variable regions (or "chameleon sequences")
                    See EXAMPLES (Prediction/Alignment/Others) > Multiple-structure sequences.

2008-05-30: Add new examples (Multiple-structure sequences: cluster 31, ..., cluster 60).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-05-24: Add new examples (Multiple-structure sequences: cluster 11, ..., cluster 30).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-05-20: New release, ProteinViewer ver. 0.5.  (fix minor bug)

2008-05-18: Add new examples (Multiple-structure sequences: cluster 1, ..., cluster 10).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-05-14: Add new examples (Fold change: 2., 3., and 4.).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-05-11: Add new examples (Fold change: 1. Addition/Deletion/Substitution ).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-05-05: New release, ComSubstruct ver. 0.5.  (print out the distribution of |LSC|/|target protein| if "-p1" is specified)

2008-05-01: New release, ComSubstruct ver. 0.4.  (support domain search: the "-p" option)

2008-04-20: New release, fragment-to-5-tile-code conversion tables of ASTRAL dataset 1.73 95% are available.
                    See PROGRAMS/NtileCodePredictor

2008-04-19: New release, ComSubstruct ver. 0.3a.  (fix a bug of incorrect output)
2008-04-19: New release, "target_ASTRAL173.code" (ASTRAL dataset 1.73) is available.
                    See PROGRAMS/ComSubstruct

2008-04-18: New release, ComSubstruct ver. 0.3.  (report more than one best matches: the "-b" option)
2008-04-17: Add new examples (ASTRAL search by ComSubstruct).
                    See EXAMPLES (Prediction/Alignment/Others).

2008-04-04: New release, ComSubstruct ver. 0.2a.  (fix a bug of output file name without '\0')
2008-04-03: New release, ComSubstruct ver. 0.2.  (support subsequence comparison. See the PROGRAMS section)

2008-04-01: New release, NtileCodePredictor ver. 0.3.  (output a ".code" file. See the PROGRAMS section)
2008-03-31: New release, ComSubstruct ver. 0.1.  (compute the longest common subsequences. See the PROGRAMS section)

2008-02-27: New release, ProteinEncoder ver. 0.7.  (support any alternative location identifier)

2008-01-30: More entries are filled in the table (EXAMPLES / Decoding / length 9).

2008-01-21: Add new examples (EXAMPLES / Encoding / Basic ideas).
2008-01-20: Add new examples (EXAMPLES / Decoding / length 9).
2008-01-19: Add new examples (EXAMPLES / Decoding / length 7).
2008-01-18: Add new examples (EXAMPLES / Decoding / length 5).

2008-01-16: New release, TetraSeqGen ver. 0.2. (Bug fix for the "-t" option)

2008-01-04: Add new examples (EXAMPLES / Alignment / Basic ideas).
2008-01-04: Add new examples (EXAMPLES / Decoding / Basic ideas).
2008-01-04: New release, TetraSeqGen ver. 0.1.
2008-01-04: New release, ProteinViewer ver. 0.4.  (support TeraSeqGen)

2008-01-02: New release, ProteinEncoder ver. 0.6.  (support artificial polygonal chains, such as straight line, self-intersections, and so on)
2008-01-02: New release, ProteinSplitter ver. 0.2.  (minor bug fix)