Gaps and PI comparisons (old)
Contents |
[edit] 1 Number of alignments in each class
The percent cutoff denotes the percentage of the total alignments excluded at a given gap cutoff.
| Total alignments | Gap cutoffs | Included alignments | Percent cutoff | |
|---|---|---|---|---|
| Ordered 85% | 355,321 | 0 | 273,415 | 23.051 |
| Disordered 85% | 130,752 | 0 | 70,613 | 45.995 |
| Ordered 60% | 4,377,058 | 4 | 4,142,855 | 5.351 |
| Disordered 60% | 946,010 | 4 | 842,646 | 10.926 |
| Ordered 40% | 14,249,207 | 10 | 13,824,348 | 2.982 |
| Disordered 40% | 3,208,833 | 10 | 2,969,997 | 7.443 |
[edit] 1.1 Leveling disordered cutoff percentage to ordered
| Original gaps | Ordered % cutoff | Original disordered % cutoff | Leveled disordered gaps | Leveled disordered % cutoff | |
|---|---|---|---|---|---|
| 85% | 0 | 23.051 | 45.995 | 1 | 23.044 |
| 60% | 4 | 5.351 | 10.926 | 6 | 5.471 |
| 40% | 10 | 2.982 | 7.443 | 17 | 2.815 |
[edit] 2 Percent identity quartiles
| Gap cutoff | 0% | 25% | 50% | 75% | 100% | |
|---|---|---|---|---|---|---|
| Ordered 85% | 0 | 85.000 | 88.136 | 91.892 | 96.512 | 99.890 |
| Disordered 85% | 0 | 85.000 | 89.091 | 92.727 | 96.000 | 99.932 |
| Ordered 60% | 4 | 60.000 | 64.368 | 69.536 | 76.351 | 99.890 |
| Disordered 60% | 4 | 60.000 | 65.000 | 71.591 | 81.250 | 99.932 |
| Ordered 40% | 10 | 40.000 | 45.833 | 52.727 | 63.333 | 99.890 |
| Disordered 40% | 10 | 40.000 | 45.455 | 52.381 | 63.333 | 99.932 |
| 0% | 25% | 50% | 75% | 100% | |
|---|---|---|---|---|---|
| Ordered 85% | 85.000 | 87.368 | 90.698 | 95.570 | 99.890 |
| Disordered 85% | 85.000 | 87.755 | 90.909 | 94.595 | 99.932 |
| Ordered 60% | 60.000 | 63.971 | 68.987 | 75.949 | 99.890 |
| Disordered 60% | 60.000 | 64.286 | 70.370 | 80.000 | 99.932 |
| Ordered 40% | 40.000 | 45.500 | 52.273 | 62.874 | 99.890 |
| Disordered 40% | 40.000 | 44.737 | 51.429 | 62.271 | 99.932 |
[edit] 3 Percent identity distributions
[edit] 3.1 40%
[edit] 3.2 60%
Note: The always-higher-pi for the disordered class comes from the right part. The gap cutoff does not seem to strongly affect the percent identity proportions.
[edit] 3.3 85%
[edit] 4 Gap distributions
Note: Very interesting, the ordered drop off curve is always sharper than the disordered drop off curve. The disordered curve is also pretty even no matter the class.
[edit] 4.1 40%
[edit] 4.2 60%
[edit] 4.3 85%
[edit] 5 Graphs of percent identity vs number of gaps
[edit] 5.1 Mean number of gaps
[edit] 5.1.1 40%
Kewl you sohuld come up with that. Excellent!
[edit] 5.1.2 85%
[edit] 5.1.3 Mean diffs stat table
Between the disordered means and and the ordered means.
| 0% | 25% | 50% | 75% | 100% | mean | sd | |
|---|---|---|---|---|---|---|---|
| 85% | 0.0868 | 0.1828 | 0.2946 | 0.3702 | 0.5065 | 0.2878 | 0.1306 |
| 60% | 0.0970 | 0.6097 | 0.7881 | 1.2211 | 1.7290 | 0.8998 | 0.4533 |
| 40% | -1.2098 | 0.4224 | 0.6878 | 0.8967 | 1.4584 | 0.6401 | 0.4124 |
[edit] 5.2 Median number of gaps
[edit] 5.2.1 40%
[edit] 5.2.2 60%
[edit] 5.2.3 85%
[edit] 5.2.4 Median diffs stat table
Between the disordered means and and the ordered medians.
| 0% | 25% | 50% | 75% | 100% | median | sd | |
|---|---|---|---|---|---|---|---|
| 85% | 0.0000 | 0.0000 | 0.0000 | 1.0000 | 1.0000 | 0.3333 | 0.4880 |
| 60% | 0.0000 | 0.0000 | 1.0000 | 1.0000 | 2.0000 | 0.9000 | 0.7089 |
| 40% | -2.0000 | 0.0000 | 0.0000 | 1.0000 | 2.0000 | 0.1833 | 0.6763 |
[edit] 5.3 Scatterplots
[edit] 5.3.1 40%
[edit] 5.3.2 60%
Cool! That's a clever way of lkooing at it!
YMMD with that asnewr! TX