- Publisher: Cambridge University Press
- Online publication date: May 2015
- Print publication year: 2015
- Online ISBN: 9781139940023
- DOI: https://doi.org/10.1017/CBO9781139940023
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. This book 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.
Nadia Pisanti - University of Pisa
Jens Stoye - Universität Bielefeld
Christina Boucher - Colorado State University
Alberto Apostolico - Georgia Institute of Technology
Paul Medvedev - Pennsylvania State University
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