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Horizontal sequence :VIRL Vertical sequence:MKF   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:   V I R L M         K         F           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).                                                                                                                                                                                                                                                                                                                                 V I R L             M           K           F           Align and score all optimal alignments here.

Horizontal sequence :VIRL Vertical sequence:MKF   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:   V I R L M         K         F           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).                                                                                                                                                                                                                                                                                                                                 V I R L             M           K           F           Align and score all optimal alignments here.

Computer Networking: A Top-Down Approach (7th Edition)
Computer Networking: A Top-Down Approach (7th Edition)
7th Edition
ISBN:9780133594140
Author:James Kurose, Keith Ross
Publisher:James Kurose, Keith Ross
Chapter1: Computer Networks And The Internet
Section: Chapter Questions
Problem R1RQ: What is the difference between a host and an end system? List several different types of end...
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Horizontal sequence :VIRL

Vertical sequence:MKF

 

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:

  V I R L
M        
K        
F        

 

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).                                                                                                                                                                                                                                                                                                                            

    V I R L
           
M          
K          
F          

Align and score all optimal alignments here. 

 

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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