Horizontal sequence :RIVL Vertical sequence:FMK   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:   R I V L F         M         K           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).                                                                                                                                                                                                                                                                                                                                 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

Curren'S Math For Meds: Dosages & Sol
11th Edition
ISBN:9781305143531
Author:CURREN
Publisher:CURREN
Chapter14: Formula Method
Section: Chapter Questions
Problem 6SST
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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. SW 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 SW 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 

Here the following points are kept into consideration  

1. The opening gap (g/o) is -3 so the first cell is written to be -3.

2. The extending gap (g/e) is -1, so the consecutive cells are increased by -1.

3. The highest from the gaps and the match and mismatch are chosen and then written. It is followed by a arrow from each in order to get the sequencing direction.

4. The scoring value is calculated by using the values from the matrix.

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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