Samenvatting

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.

Specificaties

ISBN13:9781009341233
Taal:Engels
Bindwijze:Gebonden
Aantal pagina's:487

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Inhoudsopgave

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.

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        Genome-Scale Algorithm Design