Genome-Scale Algorithm Design
Genome-Scale Algorithm Design
Djamal Belazzougui, Centre de Recherche sur l’Information Scientifique et Technique (CERIST), Algiers
Fabio Cunial, Broad Institute, Massachusetts
Alexandru I. Tomescu, University of Helsinki
$69.99
USDPresenting the fundamental algorithms and data structures that power bioinformatics workflows, this book covers a range of topics from the foundations of sequence analysis (alignments and hidden Markov models) to classical index structures (k-mer indexes, suffix arrays, and suffix trees), Burrows–Wheeler indexes, graph algorithms, network flows, and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualizations, and exercises, providing graduate students, researchers, and practitioners with a powerful algorithmic toolkit for the applications of high-throughput sequencing. An accompanying website (www.genome-scale.info) offers supporting teaching material. The second edition strengthens the toolkit by covering minimizers and other advanced data structures and their use in emerging pangenomics approaches.
- Provides an integrated picture of the fundamental algorithms and data structures that power modern sequence analysis, covering a range of topics including foundations, classical index structures, and Burrows–Wheeler indexes
- Chapters feature numerous examples, algorithm visualizations, problems, and end-of-chapter exercises, providing students with a powerful toolkit for the emerging applications of high-throughput sequencing
- Presents only the minimum data structures necessary so that students are not burdened with technical results and can also focus on more conceptual algorithm design questions
Reviews & endorsements
'This book is very effective in addressing its intended target of graduate students in bioinformatics or computer science with a well-structured but highly accessible description of the fundamental algorithms and data structures that power standard sequence analysis workflows.' Romeo Rizzi, University of Verona
Product details
September 2023Adobe eBook Reader
9781009341219
0 pages
160 b/w illus. 50 tables
This ISBN is for an eBook version which is distributed on our behalf by a third party.
Table of Contents
- Part I. Preliminaries:
- 1. Molecular biology and high-throughput sequencing
- 2. Algorithm design
- 3. Data structures
- 4. Graphs
- 5. Network flows
- Part II. Fundamentals of Biological Sequence Analysis:
- 6. Alignments
- 7. Hidden Markov models
- Part III. Genome-Scale Index Structures:
- 8. Classical indexes
- 9. Burrows–Wheeler indexes
- 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:
- 14. Haplotype analysis
- 15. Pangenomics
- 16. Transcriptomics
- 17. Metagenomics
- References
- Index.
