Scoring rules: g/o = -3, g/e = -1, match or mismatch - from PAM250 substitution matrix below.
SW algorithm.
1. Complete the scoring matrix.
Scoring matrix with PAM250 scores:
V
I
R
L
M
K
F
2. Set up, initialize and complete the SW matrix.
3. Retrace, align and score alignment(s).
Use the arrows and circles for the matrix and path(s).
V
I
R
L
M
K
F
Align and score all optimal alignments here.
PLZ the arrows and circles for the matrix and path(s) AND SHOW ALL possible Alignment
Transcribed Image Text:PAM250:
Cys
12
Ser
T Thr
-2
1
P Pro
-3
1
:0
A Ala
G Gly
-2
1
1
2
-3
1
:0
-1:1:5
N Asn
-4
1
0:-1
0: 0
D Asp
E Glu
-5
0:0 :-1
0:1
2
4
-5
-1
0: 0
1 3
4
Gln
-5
-1:0
-1
1
: 2
4
Н His
R Arg
K Lys
-3
-1
-1:0
-1
-2
1
1
-4
-1
-2
-3
-1
1
6.
-5
-1
-1
-2
1
: 1
: 3: 5
M Met
-5
-2 : -1: -2: -1
-3
-2
-3
-2
-1
-2
0: 0
6.
Ile
-2
-1 0 -2
-1
-3
-2 :-2
-2 : -2
-2: -2 -2
2
L
Leu
-6
-3
-2:-3 -2
-4 |-3
-4
-3 : -2
-2 : -3
-3
4
2
6.
V Val
-2
-1 :0 -1:0
-2
-2
-2
-2
-2
-2
-2
2
4
4
F Phe
Y Tyr
W Trp
-4
-3 : -3 : -5
-5
-5
-4 : -6 : -5: -5
-2 : -4 : -5
1
-1
-3: -3 : -5
-3: -5
-2 : -4 : -4: -4
-4: -4
-2
-1: -1: -2
7
10
-8
-2
-5
-6: -6
-7
-4
-7
-7: -5
-3: 2
-3
-4 : -5
-2
-6
17
T
P
A
G
D
E
H.
R.
K
M
V
F
Y
W
6:N
Process or set of rules that allow for the solving of specific, well-defined computational problems through a specific series of commands. This topic is fundamental in computer science, especially with regard to artificial intelligence, databases, graphics, networking, operating systems, and security.
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