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Lecture 6

The document describes the Needleman-Wunsch algorithm for sequence alignment using a DNA sequence example. It shows the step-by-step process of constructing an scoring matrix to align the sequences and determine the optimal alignment based on matching/mismatching nucleotides and gap penalties. The final matrix shows the optimal alignment score of -14.

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SUNDAS FATIMA
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50 views16 pages

Lecture 6

The document describes the Needleman-Wunsch algorithm for sequence alignment using a DNA sequence example. It shows the step-by-step process of constructing an scoring matrix to align the sequences and determine the optimal alignment based on matching/mismatching nucleotides and gap penalties. The final matrix shows the optimal alignment score of -14.

Uploaded by

SUNDAS FATIMA
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Bio Informatics

Lecture 6
Needleman–Wunsch Algorithm – Example 2

• This algorithm can be used for any two strings.


• This guide will use two small DNA sequences
as examples as shown below:
• Sequence (1): ACTGATTCA
• Sequence (2): ACGCATCA

• The length is different. The first step is to


construct a grid.
Needleman–Wunsch – Example 2
A C T G A T T C A

A
C
G
C
A
T
C
A
Needleman–Wunsch Algorithm -
Scores & Functions
 Match: +2
 Mismatch: -3
 Gap: -2
  𝑓 ( 𝑖 − 1 , 𝑗 − 1 ) + 𝑆 ( 𝑥𝑖 , 𝑦𝑖 )
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥
{ 𝑓 ( 𝑖 − 1 , 𝑗 ) + 𝑆 (𝐺𝑎𝑝)
𝑓 ( 𝑖 , 𝑗 − 1 ) + 𝑆 (𝐺𝑎𝑝)

  𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h )
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥
{ 𝑓 (  ) + 𝑆 (𝐺𝑎𝑝 )
𝑓 (  ) + 𝑆 (𝐺𝑎𝑝 )
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 ?
  𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A
C
G
{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)

C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0  -2 ?
   𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A
C
G
{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)

C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4

  
 
  𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A
C
G
{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)

C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 
𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A ?  

C
G
{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)

C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 
𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A   

{
-2
 
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
C ?
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G
C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 
𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A   

{
-2
 
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
C 
-4
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G
C
A  
?
T
C
A
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 
𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
A   

{
-2
  ?
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
C 
-4
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G -6

 
C -8

 
A -10
 
  ?
T -12

C  
-14

A 
-16
 


 
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 

  
A -2   𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
  2

{
?
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
C 
-4
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G -6

 
C -8

 
A -10
 
  ?
T -12

C  
-14

A 
-16
 


 
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 

  
A -2   𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
  2

{
0 ?
C 
-4 
  𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G -6

 
C -8

 
A -10
 
  ?
T -12

C  
-14

A 
-16
 


 
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
  
  
  
 

  
A -2   𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)
  2

{
0 -2 ? ? ? ? ? ?
C 
-4 ? 
 
? 
 
? ? ? ? ? ? ?
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G -6 ? ? ? ? ? ? ? ? ?

 
C -8 ? ? ? ? ? ? ? ? ?

 
A -10 ? ? ? ? ? ? ? ? ?
 
  ?
T -12 ? ? ? ? ? ? ? ? ?
C  
-14 ? ? ? ? ? ? ? ? ?
A 
-16
  ? ? ? ? ? ? ? ? ?


 
Needleman–Wunsch – Example 2
A C T G A T T C A Match: +2; Mismatch: -3; Gap: -2;
0 -2 -4 -6 -8 -10 -12 -14 -16 -18

  
  
  
  
  
      
 

  
A -2 -14   𝑓 (  ) +𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

{
  2 0 -2 -4 -6 -8 -10 -12

C 
-4 0

 
4

 
2 0 -2 -4 -6 -8 -10
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
  𝑓 (  ) +𝑆(𝐺𝑎𝑝)
G -6 -2 2 1 4 2 0 -2 -4 -6

 
C -8 -4 0 -1 2 1 -1 -3 0 -2

 
A -10 -6 -2 -3 0 4 2 0 -2 2
 
  ?
T -12 -8 -4 0 -2 2 6 4 2 0

C  
-14 -10 -6 -2 -4 0 4 2 6 4

A 
-16
  -12 -8 -4 -5 -2 2 1 4 8


 
Needleman–Wunsch Algorithm - Scores &
Functions

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