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

Veli Antti Tapani Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru Ioan Tomescu

Research output: Book/ReportBookScientificpeer-review

Abstract

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.

Highlights:
- Provides an integrated picture of the fundamental algorithms and data structures that power modern sequence analysis, covering a range of topics that include foundations, classical index structures and Burrows-Wheeler indexes.
- Features 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 setup of data structures necessary to understand the advanced concepts, so that students are not burdened with technical results and can also focus on more conceptual algorithm design questions.
Original languageEnglish
PublisherCambrigde University Press
Number of pages391
ISBN (Print)9781107078536
ISBN (Electronic)9781139940023
Publication statusPublished - May 2015
MoE publication typeC1 Scientific book

Fields of Science

  • 113 Computer and information sciences
  • 1184 Genetics, developmental biology, physiology

Cite this

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abstract = "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.Highlights:- Provides an integrated picture of the fundamental algorithms and data structures that power modern sequence analysis, covering a range of topics that include foundations, classical index structures and Burrows-Wheeler indexes.- Features 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 setup of data structures necessary to understand the advanced concepts, so that students are not burdened with technical results and can also focus on more conceptual algorithm design questions.",
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Genome-Scale Algorithm Design : Biological Sequence Analysis in the Era of High-Throughput Sequencing. / Mäkinen, Veli Antti Tapani; Belazzougui, Djamal; Cunial, Fabio; Tomescu, Alexandru Ioan.

Cambrigde University Press, 2015. 391 p.

Research output: Book/ReportBookScientificpeer-review

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AB - 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.Highlights:- Provides an integrated picture of the fundamental algorithms and data structures that power modern sequence analysis, covering a range of topics that include foundations, classical index structures and Burrows-Wheeler indexes.- Features 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 setup of data structures necessary to understand the advanced concepts, so that students are not burdened with technical results and can also focus on more conceptual algorithm design questions.

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