Bioinformatics

Lecture -05

Nadia Afrin Ritu

Lecturer, Computer Science and Engineering
Chapter 2-The Smith-Waterman Algorithm
The Smith-Waterman Algorithm

Local Alignment

✓Dynamic Programming
Problems Sub-problems Optimal solution
Continued

• This algorithm is similar to Needleman-Wunsch algorithm.

• In Needleman-Wunsch algorithm, we perform the complete matching.
• Where as in Smith-Waterman we just make limit the min possible
score for every cell to zero i.e. all negative values which we get in
Needleman-Wunsch is replaced by zero.

© Bioinformatics| Nadia Afrin Ritu

Continued

The Smith-Waterman Algorithm consists of 3 Stages:

1. Initialization
2. Matrix Filling
3. Trace Back

© Bioinformatics| Nadia Afrin Ritu

 Stage 1

© Bioinformatics| Nadia Afrin Ritu

Stage 2
Stage 3
Local Alignment-Example1
Matrix Filling
Matrix Filling
Traceback
Alignment
Why Local Alignment?
• When working with long sequences of many thousands, or even
millions, of nucleotides, local alignment methods can identify
subsequence matches that would be impossible to find using global or
semiglobal alignments.