Horizontal sequence :RIVL Vertical sequence:FMK   Scoring rules: g/o = -3, g/e = -1, match or mismatch - from PAM250 substitution matrix below.  NW algorithm.    1. Complete the scoring matrix.    Scoring matrix with PAM250 scores:   R I V L F         M         K           2. Set up, initialize and complete the NW matrix.  3. Retrace, align and score alignment(s).             Use the arrows and circles for the matrix and path(s).                                                                                                                                                                                                                                                                                                                                 R I V L             F           M           K           Align and score all optimal alignments here.  PLZ  the arrows and circles for the matrix and path(s) AND SHOW ALL possible Alignment

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Author:James Kurose, Keith Ross
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Horizontal sequence :RIVL

Vertical sequence:FMK

 

Scoring rules: g/o = -3, g/e = -1, match or mismatch - from PAM250 substitution matrix below. 

  1. NW algorithm

 

1. Complete the scoring matrix. 

 

Scoring matrix with PAM250 scores:

  R I V L
F        
M        
K        

 

2. Set up, initialize and complete the NW matrix

3. Retrace, align and score alignment(s).            

Use the arrows and circles for the matrix and path(s).                                                                                                                                                                                                                                                                                                                            

    R I V L
           
F          
M          
K          

Align and score all optimal alignments here. 

PLZ  the arrows and circles for the matrix and path(s) AND SHOW ALL possible Alignment 

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
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
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