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Algorithms on Strings, Trees and Sequences by Dan Gusfield

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11

Core String Edits, Alignments, and Dynamic Programming

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11.1. Introduction

In this chapter we consider the inexact matching and alignment problems that form the core of the field of inexact matching and others that illustrate the most general techniques. Some of those problems and techniques will be further refined and extended in the next chapters. We start with a detailed examination of the most classic inexact matching problem solved by dynamic programming, the edit distance problem. The motivation for inexact matching (and, more generally, sequence comparison) in molecular biology will be a recurring theme explored throughout the rest of ...

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