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Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing

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 visualisations, 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

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

400 pages, 90 b/w illustrations, 4 tables

Cambridge University Press

Hardback | May 2015 | #220323 | ISBN-13: 9781107078536
Availability: Usually dispatched within 6 days Details
NHBS Price: £40.99 $52/€49 approx

About this book

High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. Genome-Scale Algorithm Design provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows–Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.


Contents

Notation
Preface

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 (HMMs)

Part III. Genome-Scale Index Structures:
8. Classical indexes
9. Burrows–Wheeler indexes

Part IV. Genome-Scale Algorithms:
10. Read alignment
11. Genome analysis and comparison
12. Genome compression
13. Fragment assembly

Part V. Applications:
14. Genomics
15. Transcriptomics
16. Metagenomics
References
Index


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Biography

Veli Mäkinen is a Professor of Computer Science at the University of Helsinki, Finland, where he heads a research group working on genome-scale algorithms as part of the Finnish Center of Excellence in Cancer Genetics Research. He has taught advanced courses on string processing, data compression, biological sequence analysis, along with introductory courses on bioinformatics.

Djamal Belazzougui is a postdoctoral researcher at the University of Helsinki. His research topics include hashing, succinct and compressed data structures and string algorithms.

Fabio Cunial is a postdoctoral researcher at the University of Helsinki. His research focuses on string algorithms and genome analysis.

Alexandru I. Tomescu is a postdoctoral researcher at the University of Helsinki. His current research interests lie at the intersection of computational biology and computer science.

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