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8a. We used the scoring scheme given in Section 3.2. That is, for a pair of symbols
and b,
s
(
a
,
b
)
=
+
1
if
a =
b
,
s
(
a
,
b
)
=
1
if
a
b
,
s
(
a
,
_
)
=
2
,
s
(
_,
a
)
=
2
,
s
(
_,
_
)
=
0
, where _ represents a gap.
105 104 104 106 105 104 104 106 105 104 104 106 5 4 5 5 40 40
… 27 18 50 27 2 : A
3 3 2 3 3 2 3 3 2 : B
2 3 5 6 6 112 112 19 128 9 9 5 9 9 5 112 4 5 5 5 5 : C
5 6 112 112 19 128 41 105 104 104 106 61 5 50 27 18 : D
Fig. 10. Macros in group G1
A C 0
A 3 2 3 3 3 2 3 C 0
A 3 3 2 C 0
A 3 3 2 3 3 D 2 B B 3 C 0
A B 3 C 0
A B B B C 0
A B B + C 0
A 3 3 2 B B + C 0
A B B 3 C 0
Fig. 11. Sequences in G1 after macros substitution
Fig. 12. Sequences in G1 after multiple alignment
A finite automaton is constructed from the result of the multiple alignment as was
described in Section 3.3. Figure 13 shows the finite automaton constructed from fig-
ure 12.
The performance of the finite automaton was tested with 47 normal sequences and
34 abnormal sequences as mentioned at the beginning of this section. We used the
scoring scheme illustrated in Section 3.3. That is, a legitimate move is worth 3 points,
a gap-move is worth -1 points, skipping -3 points, and the threshold is 0.
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