CSE 589Applied AlgorithmsSpring 1999

Table of Contents

CSE 589Applied AlgorithmsSpring 1999

DNA

Approximate Matching

Applications of Approximate Matching

Scoring an Approximate Matching

Scoring Example

Approximate String Matching Problem

Algorithms for Approximate String Matching

Dynamic Programming for Approximate String Matching

Max Score Recurrence

Dynamic Program Initialization

The Dynamic Programming Pattern

Dynamic Program Example (1)

Dynamic Program Example (2)

Dynamic Program Example (3)

Dynamic Program Example (4)

Dynamic Program Example (5)

Dynamic Programming Order

How to Find the Matching

Computing the Matching Graph (1)

Computing the Matching Graph (2)

Computing the Matching Graph (3)

Computing the Matching Graph

Computing the Matching Path

Algorithm to find Matching

Computing the Matching

Creating the Matching

Example of Multiple Paths

Approximate String Searching

Search Algorithm

Example of Approximate Matching

Recovering the Matchings

Notes on Approximate Matching

DNA Sequence Reconstruction

Tagging the Clones

Problem to Solve

Contiguous Ordering Problem

Contiguous Ordering Solutions

Linear Time Algorithm

DNA Downside

PQ Trees

Example PQ-Tree

Equivalent PQ Trees

Orderings Defined by a PQ Tree

PQ Tree Solution for the Contiguous Ordering Problem

Example (1)

Example (2)

Example (3)

Example (4)

Example (5)

Example (6)

Example (7)

Example (8)

Example (9)

Example (10)

Example (11)

Example (12)

Email: ladner@cs.washington.edu

Home Page: http://www.cs.washington.edu/education/courses/589/CurrentQtr/

Other information:
CSE 589: Applied Algorithms

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