Bioinformatics Analysis:Smith Waterman Algorithm

Demonstration of SmithWaterman Algorithm

In this tutorial I've demonstrated the implementation of SmithWaterman Algorithm.

The Smith Waterman algorithm is a dynamic programming algorithm that builds a real or implicit array where each cell of the array represents a sub problem in the alignment problem discovered by Smith and Waterman in 1981.

Part 1

Part 2

Part 3

Smith Waterman Algorithm

This Algorithm takes alignments of any length, at any location, in any sequence, and determines whether an optimal alignment can be found. Based on these calculations, scores or weights are assigned to each character to character comparison.

• Positive for exact matches/substitutions.
• Negative for insertions/deletions.
• In weight matrices, scores are added together and the highest scoring alignment is reported.

Goal of Smith Waterman Algorithm

It finds solutions to smaller pieces of the problem and then puts them all together to form a complete and optimal final solution to the entire problem.

Why Smith Waterman Algorithm is superior to other Algorithms?

1. It is superior to the BLAST and FASTA algorithms because it searches a larger field of possibilities.
2. It is a more sensitive technique in aligning the sequences.
3. Instead of looking at the entire sequence at once,Smith Waterman compares multi lengthed segments.
4. The algorithm itself is recursive in nature.

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