Bio Informatics

Lecture 7
 Smith-Waterman Algorithm – Example
(Local Alignment)
• The basic steps for the algorithm are similar to
that of Needleman-Wunsch algorithm.
• The steps are:
• 1. Initialization of a matrix.
2. Matrix Filling with the appropriate scores.
3. Trace back the sequences for a suitable
alignment.
 Smith-Waterman Algorithm – Example
(Local Alignment)
• This algorithm can be used for any two strings.
• This guide will use two small DNA sequences
as examples as shown below:
• Sequence (1): CGTGAATTCAT
• Sequence (2): GACTTAC

• The length is different. The first step is to

construct a grid.
 Smith-Waterman – Example
C G T G A A T T C A T

G
A
C
T
T
A
C
 Smith-Waterman Algorithm - Scores
& Functions
 Match: +5
 Mismatch: -3
 Gap: -4
  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: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T
0 ?
G
A
 
C ?
T
T
A
C
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T
0 0 0 0 0 0 0 0 0 0 0 0
G 0
A 0
 
C 0 ?
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 ?
A 0
C 0
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 ?
A 0
C 0
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0  5

A 0 ?
C 0
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0  5

A 0 0
C 0 ?
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0   5

A 0 0 ?
C 0  5
T 0
T 0
A 0
C 0
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0  5 ? ? ? ? ? ? ? ? ?
A 0 0  1
  ? ? ? ? ? ? ? ? ?
C 0
  5 ? ? ? ? ? ? ? ? ? ?
T 0 ? ? ? ? ? ? ? ? ? ? ?
T 0 ? ? ? ? ? ? ? ? ? ? ?
A 0 ? ? ? ? ? ? ? ? ? ? ?
C 0 ? ? ? ? ? ? ? ? ? ? ?
 Smith-Waterman – Example
  𝑓 (  ) +𝑆(𝑚𝑎𝑡𝑐h 𝑂𝑅 𝑚𝑖𝑠𝑚𝑎𝑡𝑐h)

Match: +5; Mismatch: -3; Gap: -4;

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

C G T G A A T T C A T  
?
0 0 0 0 0 0 0 0 0 0 0 0
G 0 0  5 1 5 1 0 0 0 0 0 0
A 0 0   1 2 1 10 6 2 0 0 5 1
C 0
  5 1 0 0 6 7 3 0 5 1 2
T 0 1 2 6 2 2 3 12 8 4 2 6
T 0 0 0 7 3 0 0 8 17 13 9 7
A 0 0 0 3 4 8 5 4 13 14 18 14
C 0 5 1 0 0 4 5 2 9 18 14 15
Smith-Waterman Algorithm - Alignments
Smith-Waterman Algorithm - Alignments