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
AUD$106.95
inc GSTPresenting 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
October 2023Hardback
9781009341233
487 pages
250 × 175 × 30 mm
0.98kg
160 b/w illus. 50 tables
Available
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.
