1. RNA 2nd
structure comparison

2. Structure comparison
TP
FP
TN
FN
●
Consider the structure as being a set of
1. positions over the alphabet {(,),.})
2. unpaired and paired positions
. . . .
. . . .
. . . .
(2
(1
)1
)2
(1
)1
(2
)2
(1
)1
(2
)2
P N
T
2 3
0 3
F
2 1
4 1

3. Sensitivity + Specificity
sensitivity =
TP
TP + FN
specificity =
TN
TN + FP
●
Sensitivity relates to the test's ability to identify
positive results
●
Specificity relates to the ability of the test to identify
negative results

4. Sensitivity + Specificity
. . . .
. . . .
. . . .
(2
(1
)1
)2
(1
)1
(2
)2
(1
)1
(2
)2
P N sens
T
2 3 0.67
0 3 0.00
F
2 1 0.60
4 1 0.43
spec
sensitivity =
TP
TP + FN
specificity =
TN
TN + FP

5. Matthews correlation coefficient
. . . .
. . . .
. . . .
(2
(1
)1
)2
(1
)1
(2
)2
(1
)1
(2
)2
P N MCC
T
2 3 0.26
0 3 -0.38
F
2 1
4 1
MCC =
TP ⋅TN − FP ⋅FN
√(TP + FN)⋅(TN + FP)⋅(TP + FP )⋅(TN + FN )

6. Structure comparison
P N sens MCC
T
15 8 0.79 0.02
4 8 0.50 -0.28
F
27 4 0.23
38 4 0.17
spec
P N sens MCC
T
12 27 0.63 0.40
6 27 0.46 0.11
F
8 7 0.77
14 7 0.66
spec

7. RNA 2nd
structure metrics
S1
( . . . . . . )
S2
. . ( . . ) . .
S . . . . . . . .
distance(S1
, S) = distance (S2
, S) ?
distance(S1
, S) ≠ distance (S2
, S) ?
● Different metrics – different characteristics
●
Moulton et al. (2000)