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
- Part V Applications
- 14 Haplotype analysis
- 15 Pangenomics
- 16 Transcriptomics
- 17 Metagenomics
- References
- Index
14 - Haplotype analysis
from Part V - Applications
Published online by Cambridge University Press: 28 September 2023
- 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
- Part V Applications
- 14 Haplotype analysis
- 15 Pangenomics
- 16 Transcriptomics
- 17 Metagenomics
- References
- Index
Summary
With diploid organisms, one is interested not only in discovering variants but also in discovering to which of the two haplotypes each variant belongs. One would thus like to identify the variants that are co-located on the same haplotype, a process called haplotype phasing. Assume we have managed to do haplotype phasing for several individuals. It is then of interest to do haplotype matching, that is, to locate long contiguous blocks shared by multiple individuals. The chapter covers algorithms and complexity analysis of these key haplotype analysis tasks. A close connection between classical indexes and a tailored data structure called the positional BWT index is established.
- Type
- Chapter
- Information
- Genome-Scale Algorithm DesignBioinformatics in the Era of High-Throughput Sequencing, pp. 333 - 343Publisher: Cambridge University PressPrint publication year: 2023