18.417 - Lecture 3

Review - Dynamic Programming

Why dynamic programming

From Global to Local alignments

0. Setting up the scoring matrix

1. Allowing gaps in s

2. Allowing gaps in t

3. Allowing mismatches

4. Choosing optimal paths

5. Rewarding matches

From Global to Local alignments

Semi-Global Motivation

Ignoring starting gaps

Ignoring trailing gaps

Using the new scoring scheme

Semi-global alignments

Semi-Global Alignment

From Global to Local alignments

Intro to Local Alignments

Global Alignment

Local Alignment

Local Alignment issues

From Global to Local alignments

Motivation for affine gap penalty

Additional Matrices

Update rules

Simplified rules

General Gap Penalty

From Global to Local alignments

Dynamic Programming Versatility

DP Algorithm Variations

What’s next