Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing

The fundamental algorithms and data structures that power standard bioscience workflows, with rigorous computer science formulations.

Veli Mäkinen (Author), Djamal Belazzougui (Author), Fabio Cunial (Author), Alexandru I. Tomescu (Author)

9781009341233, Cambridge University Press

Hardback, published 12 October 2023

470 pages, 160 b/w illus. 50 tables
25 x 17.5 x 3 cm, 0.98 kg

'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

Presenting 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.

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.

Subject Areas: Data mining [UNF]