Bioinformatics -

1. 1
SIDDAGANGA INSTITUTE OF TECHNOLOGY
Department of Biotechnology
B.E. Biotechnology
Local Alignment
Mr. Vivek Chandramohan
Bioinformatics – Local Alignment
Assistant professor
Department of Biotechnology
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

2. 2
Local Alignment
Smith–Waterman algorithm
 No negative scores are used
 A similar tracing-back procedure is used in dynamic programming
 It starts with the highest scoring position and proceeds diagonally up to the
left until reaching a cell with a zero
 LALIGN - web-based Local alignment program
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

3. 3
Local Alignment
Smith–Waterman algorithm
 Three steps in dynamic programming
 Initialization
 Matrix fill (scoring)
 Traceback (alignment)
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

4. 4
Local Alignment
Smith–Waterman algorithm
Seq1 A T G A T G T A G
Seq2 G A G A T G T G C
Initialization
 Sequence Seq1 is first row
 Sequence seq2 is first Column
 Gap value in 2nd row for S1 sequences
 Gap value in 2nd Column for S2 sequences
Match : 2, Mismatch : -1, Gap : -2
S1/s2 0 A T G A
0 0 0 0 0 0
G 0
A 0
G 0
A 0
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

5. 5
Matrix fill (scoring)
Match : 2, Mismatch : -1, Gap : -2
S/T 0 A T G A T G T A G
0 0 0 0 0 0 0 0 0 0 0
G 0 0 0
A 0
G 0
A 0
T 0
G 0
T 0
G 0
C 0
0 + -1 0 + -2
0 + -2 0
0 + 2 = 0
0 + -2 = 0
0 + -2 = 0
0 + 2 0 +-2
0 + -2 2
0 + 2 = 2
0 + -2 = 0
0 + -2 = 0
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

6. 6
Matrix fill (scoring)
Match : 2, Mismatch : -1, Gap : -2
S/T 0 A T G A T G T A G
0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 2 0 0 2 0 0 0
A 0 2 0 0 4 2 0 0 2 0
G 0 0 1 2 2 3 4 2 0 4
A 0 2 0 0 4 2 2 2 4 2
T 0 0 4 2 2 6 4 4 2 3
G 0 0 2 6 4 4 8 6 4 4
T 0 0 2 4 4 6 6 10 8 6
G 0 0 0 4 3 4 8 8 9 10
C 0 0 0 2 3 1 6 7 7 8
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

7. Trace back
7
Match : 2, Mismatch : -1, Gap : -2
S/T 0 A T G A T G T A G
0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 2 0 0 2 0 0 0
A 0 2 0 0 4 2 0 0 2 0
G 0 0 1 2 2 3 4 2 0 4
A 0 2 0 0 4 2 2 2 4 2
T 0 0 4 2 2 6 4 4 2 3
G 0 0 2 6 4 4 8 6 4 4
T 0 0 2 4 4 6 6 10 8 6
G 0 0 0 4 3 4 8 8 9 10
C 0 0 0 2 3 1 6 7 7 8
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka

8. Alignment
8
G A T G T A G
| | | | | | |
G A T G T - G
2 2 2 2 2 -2 2
6 X 2 = 12
1 X -2 = -2
10
G A T G T
| | | | |
G A T G T
2 2 2 2 2
5 X 2 = 10
10
B.E. Biotechnology, Department of Biotechnology, SIT, Tumkur, Karnataka