|
(A) Tetrapod Myoglobin
|
|---|
| |
GCTMPCA (ε = 0.70)
|
LnLCorr99
|
LnLCorr07
|
Ancestral States
|
CoMap
| | |
|---|
| |
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
χ
2
|
p – value
|
|---|
|
(i,i+3)
|
0
|
53
|
1
|
5
|
0
|
7
|
2
|
51
|
0
|
9
|
7.51
|
1.11 × 10-1
|
|
(i,i+4)
|
10
|
43
|
0
|
6
|
0
|
7
|
4
|
49
|
0
|
9
|
6.75
|
1.50 × 10-1
|
|
(B) Randomized Tetrapod Myoglobin
|
| |
GCTMPCA (ε = 0.70)
|
LnLCorr99
|
LnLCorr07
|
Ancestral States
|
CoMap
| | |
| |
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
χ
2
|
p – value
|
|
(i,i+3)
|
1
|
52
|
0
|
6
|
0
|
7
|
0
|
53
|
0
|
9
|
1.43
|
8.40 × 10-1
|
|
(i,i+4)
|
0
|
53
|
0
|
6
|
0
|
7
|
0
|
53
|
0
|
9
|
n/a
|
n/a
|
|
(C) Chordate Myosin
|
| |
GCTMPCA (ε = 0.70)
|
LnLCorr99
|
LnLCorr07
|
Ancestral States
|
CoMap
| | |
| |
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
χ
2
|
p – value
|
|
(i,i+3)
|
-
|
-
|
5
|
1
|
-
|
-
|
41
|
12
|
8
|
1
|
0.69
|
7.09 × 10-1
|
|
(i,i+4)
|
-
|
-
|
2
|
4
|
-
|
-
|
48
|
5
|
8
|
1
|
14.18
|
8.33 × 10
-3
|
|
(D) Randomized Chordate Myosin
|
| |
GCTMPCA (ε = 0.70)
|
LnLCorr99
|
LnLCorr07
|
Ancestral States
|
CoMap
| | |
| |
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
p ≤ α
|
p > α
|
χ
2
|
p – value
|
|
(i,i+3)
|
-
|
-
|
0
|
6
|
-
|
-
|
7
|
46
|
0
|
9
|
2.21
|
3.31 × 10-1
|
|
(i,i+4)
|
-
|
-
|
0
|
6
|
-
|
-
|
0
|
53
|
0
|
9
|
n/a
|
n/a
|
- χ2 goodness-of-fit tests comparing the performance of tree-aware methods for detecting alpha helix periodicity at (i, i + 3) and (i, i + 4). Counts are calculated for GCTMPCA with the empirically validated optimal ε = 0.70. In most cases, there is no statistically significant difference in performance between the tree-aware methods with the single exception being (i, i+ 4) in myosin, where AS and CoMap out-perform LnLCorr99. Data is not presented on the myosin alignment for tree-aware methods which proved too computationally intensive to be practical. Counts in Table 2 can be directly compared with counts in Table 3. α = 0.01.
