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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.  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).

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).

Database System Concepts
Database System Concepts
7th Edition
ISBN:9780078022159
Author:Abraham Silberschatz Professor, Henry F. Korth, S. Sudarshan
Publisher:Abraham Silberschatz Professor, Henry F. Korth, S. Sudarshan
Chapter1: Introduction
Section: Chapter Questions
Problem 1PE
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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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