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Lecture 9

The Smith-Waterman algorithm is used for local sequence alignment to find similar regions between two nucleotide or protein sequences. It involves constructing a matrix where the edges are initialized to 0 instead of increasing gap penalties. Scores are filled into the matrix based on matches, mismatches and gaps. The traceback starts from the highest score and ends at a score of 0, finding the optimal local alignment between the sequences. As an example, the algorithm is demonstrated aligning the protein sequences "COELACANTH" and "PELICAN".

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36 views24 pages

Lecture 9

The Smith-Waterman algorithm is used for local sequence alignment to find similar regions between two nucleotide or protein sequences. It involves constructing a matrix where the edges are initialized to 0 instead of increasing gap penalties. Scores are filled into the matrix based on matches, mismatches and gaps. The traceback starts from the highest score and ends at a score of 0, finding the optimal local alignment between the sequences. As an example, the algorithm is demonstrated aligning the protein sequences "COELACANTH" and "PELICAN".

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 9
Smith-Waterman Algorithm – Example 3
(Local Alignment)
• The basic steps for the algorithm are similar to that of Needleman-
Wunsch algorithm.
• The steps are:
• The edges of the matrix are initialized to 0 instead of increasing
gap penalties. (Initialization of matrix)
• The maximum score is never less than 0, and no pointer is
recorded unless the score is greater than 0. (Matrix Filling with the
appropriate scores)
• The trace-back starts from the highest score in the matrix (rather
than at the end of the matrix) and ends at a score of 0 (rather than
the start of the matrix). (Trace back the sequences for a suitable
alignment)
Smith-Waterman Algorithm – Example 3
(Local Alignment)
• This algorithm can be used for any two strings.
• This guide will use two small Protein
sequences as examples as shown below:
• Sequence (1): COELACANTH
• Sequence (2): PELICAN
• The length is different. The first step is to
construct a grid.
Smith-Waterman – Example 3
C O E L A C A N T H

P
E
L
I
C
A
N
Smith-Waterman Algorithm - Scores
& Functions
 Match: +1
 Mismatch: -1
 Gap: -1
  𝑓 ( 𝑖 − 1 , 𝑗 − 1 ) + 𝑆 ( 𝑥𝑖 , 𝑦 𝑖 )
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥
{ 𝑓 ( 𝑖 − 1 , 𝑗 ) + 𝑆 (𝐺𝑎𝑝)
𝑓 ( 𝑖 , 𝑗 − 1 ) + 𝑆 (𝐺𝑎𝑝)
0

  𝑓 (  ) + 𝑆 (𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h )
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥
{ 𝑓 (  ) + 𝑆 (𝐺𝑎𝑝 )
𝑓 (  ) + 𝑆 (𝐺𝑎𝑝 )
0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 ?
P
E
 
L ?
I
C
A
N
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P ?
E
 
L ?
I
C
A
N
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 ?
E 0
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 ?
E 0
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0
E 0 ?
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0
E 0 0 ?
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0 ?
E 0 0 0
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0 0
E 0 0 0 ?
 
L 0 ?
I 0
C 0
A 0
N 0
Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +1; Mismatch: -1; Gap: -1;


{
𝑓 ( 𝑖 , 𝑗 ) =𝑚𝑎𝑥 𝑓 (  ) +𝑆(𝐺𝑎𝑝)
𝑓 (  ) +𝑆(𝐺𝑎𝑝)
0

C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0 0 ? ? ? ? ? ? ?
E 0 0 0
  1 ? ? ? ? ? ? ?
 
L 0 ? ? ? ? ? ? ? ? ? ? ?
I 0 ? ? ? ? ? ? ? ? ? ?
C 0 ? ? ? ? ? ? ? ? ? ?
A 0 ? ? ? ? ? ? ? ? ? ?
N 0 ? ? ? ? ? ? ? ? ? ?
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0
  1 0 0 0 0 0 0 0
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0
P 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0
  1 0 0 0 0 0 0 0
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 N
P 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0
  1 0 0 0 0 0 0 0 N
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 AN
P 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0
  1 0 0 0 0 0 0 0 AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 C AN
P 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0
  1 0 0 0 0 0 0 0 C AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 A C AN
P 0 0 0 0 0 0 0 0 0 0 0 .
E 0 0 0
  1 0 0 0 0 0 0 0 I C AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 L A C AN
P 0 0 0 0 0 0 0 0 0 0 0 .
E 0 0 0
  1 0 0 0 0 0 0 0 L I C AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 E L A C AN
P 0 0 0 0 0 0 0 0 0 0 0 .
E 0 0 0
  1 0 0 0 0 0 0 0 E L I C AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0
   
C 0 1 0 0 0 0  2 1 0 0 0

A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman – Example

Match: +1; Mismatch: -1; Gap: -1;


C O E L A C A N T H
0 0 0 0 0 0 0 0 0 0 0 E L A C AN
P 0 0 0 0 0 0 0 0 0 0 0 .
E 0 0 0
  1 0 0 0 0 0 0 0 E L I C AN
L 0 0 0 0  2 1 0 0 0 0 0
I 0 0 0 0  1 
 
1 0 0 0 0 0 =+1+1-1+1+1+1
   
C 0 1 0 0 0 0  2 1 0 0

0 =4
A 0 0 0 0 0 1 0   3 2 1 0

 
N 0 0 0 0 0 0 0 2  
4 
3 2

  
 

  
 
Smith-Waterman Algorithm - Tasks &
Homeworks
 Mandatory Task: Provide all possible
alignments to these DNA sequences.
 The task is assigned on LMS page.
 The material of the lecture will be shared on
LMS page.

 Good Luck and Thank You!

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