Cite as: Cold Spring Harb. Protoc.; 2007; doi:10.1101/pdb.top31

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topic_introductionTopic Introduction

Dot Matrix Pairwise Sequence Comparison

David W. Mount

Adapted from "Alignment of Pairs of Sequences," Chapter 3, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.


INTRODUCTION

A dot matrix analysis is primarily a method for comparing two sequences to look for possible alignment of characters between the sequences. The method is also used for finding direct or inverted repeats in protein and DNA sequences, and for predicting regions in RNA that are self-complementary and that, therefore, have the potential of forming secondary structure through base-pairing.


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