Biology Reference
In-Depth Information
Table 9.5
The set of parameters of a HMM describing a DNA sequence. The model incorporates information about din-
ucleotide frequencies. Here the block matrices
P
+
and
P
−
are the “+” and “
−
” transition matrices from Table
9.1
The
process remains in the the “+” and “
−
” region with probabilities
p
and
q
, respectively. When switching between the “+”
and “
−
” regions, this model assumes that all states in the new region are equally likely. For each of the emission symbols
k
∈
M
, the model assumes that only the states
k
+
and
k
−
from can
Q
emit
k
. The initial distribution is uniform.
Transitions
Emissions
Initial
A
+
C
+
T
+
G
+
A
−
C
−
T
−
G
−
A
C
T
G
A
+
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
1
0
0
0
0.125
C
+
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
0
1
0
0
0.125
(P
+
)
∗
p
T
+
(1−
p
)/4
(1−
p
)/4
(1−
p
)/4
(1−
p
)/4
0
0
1
0
0.125
G
+
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
(1
−
p
)/4
0
0
0
1
0.125
A
−
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
1
0
0
0
0.125
C
−
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
0
1
0
0
0.125
P
−
)
∗
T
−
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
(1
−
q
)/4
(
q
0
0
1
0
0.125
G
−
(1−
q
)/4
(1−
q
)/4
(1−
q
)/4
(1−
q
)/4
0
0
0
1
0.125
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