|
Why is
iDNA
a toy?
Consider the
following sequences. Compare observations with predictions
using simultaneous and sequential rotations and with the
roll and tilt axes swapped.
|
Sequence
|
Source
|
Observed
|
M
|
Q
|
q
|
m
|
|
TC(GA3T3C)37GA
|
Hagerman
|
Straight
|
S
|
S
|
S
|
S
|
|
TT(A4T4)37AA
|
Hagerman
|
Straight
|
S
|
S
|
S
|
S
|
|
(G3A3T3C3)25
|
Hagerman
|
Straight
|
S
|
S
|
S
|
S
|
|
(G2A4T4C2)25
|
Hagerman
|
Straight
|
S
|
S
|
S
|
S
|
|
(GGA3T3CC)30
|
Hagerman
|
Curved
|
C
|
C
|
C
|
C
|
|
(GA4T4C)30
|
Hagerman
|
Curved
|
C
|
s
|
C
|
s
|
|
(G3C3(TAGAG4C3)2TAGA)4
|
Harrington
et al
|
Curved
|
s
|
C
|
s
|
C
|
|
((CG)3A5(CG)3A4)7
|
Trifonov
|
Curved
|
C
|
CC
|
C
|
CC
|
Keys:
|
M
|
Prediction
- Simultaneous: Z(twist),Y(roll),X(tilt)
|
|
Q
|
Prediction
- Sequential: Z(twist).Y(roll).X(tilt)
|
|
q
|
Prediction
- Sequential: Z(twist).Y(tilt).X(roll)
|
|
m
|
Prediction
- Simultaneous: Z(twist),Y(tilt),X(roll)
|
|
C
|
curved
predicted
|
|
CC
|
near
circle predicted
|
|
S
|
straight
predicted
|
|
s
|
straight
predicted incorrectly
|
|
c
|
curved
predicted incrorrectly
|
Note:
- The rotation
procedure used in Augur was q
- The default
rotation procedure in iDNA
is Q
- All rotation
procedures produce essentially the same results when the
sequence is straight. There is no known case of
c!
- The
simultaneous and sequential rotations produce very
similar results when the tilt and roll axes are swapped:
M
= q
and Q
= m.
- The best
match to the Hagerman anomalous gel mobility data is
provided by M
or q.
- The Trifonov
and the Harrington et al examples are best matched by
Q
or m.
|
