Book contents
- Frontmatter
- Dedication
- Contents
- List of insights
- Preface
- Notation
- Part I Preliminaries
- Part II Fundamentals of Biological Sequence Analysis
- Part III Genome-Scale Index Structures
- Part IV Genome-Scale Algorithms
- 10 Alignment-based genome analysis
- 11 Alignment-free genome analysis and comparison
- 12 Compression of genome collections
- 13 Fragment assembly
- Part V Applications
- References
- Index
11 - Alignment-free genome analysis and comparison
from Part IV - Genome-Scale Algorithms
Published online by Cambridge University Press: 28 September 2023
Book contents
- Frontmatter
- Dedication
- Contents
- List of insights
- Preface
- Notation
- Part I Preliminaries
- Part II Fundamentals of Biological Sequence Analysis
- Part III Genome-Scale Index Structures
- Part IV Genome-Scale Algorithms
- 10 Alignment-based genome analysis
- 11 Alignment-free genome analysis and comparison
- 12 Compression of genome collections
- 13 Fragment assembly
- Part V Applications
- References
- Index
Summary
This chapter shows how to perform analysis and comparison of genomes without assuming a reference genome to be available. The bidirectional BWT index turns out to be essential here, and the chapter covers a comprehensive set of techniques to manipulate this data structure. The algorithms covered include computing maximal exact/unique matches, substring kernels, matching statistics, and Jaccard similarity.
- Type
- Chapter
- Information
- Genome-Scale Algorithm DesignBioinformatics in the Era of High-Throughput Sequencing, pp. 240 - 283Publisher: Cambridge University PressPrint publication year: 2023