Genome-Scale Algorithm Design Biological Sequence Analysis Era… 9781107078536 LN

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Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput SequencingVeli Mäkinen, Fabio Cunial, Alexandru I. Tomescu, Djamal Belazzougui

Cambridge University PressHardcover

Unused and unread, minor cosmetic imperfections such as scuffing or minor creasing. Stamped 'damaged' by publisher to a non-text page.

EAN: 9781107078536Published 07/05/2015Language: English

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.

NotationPrefacePart I. Preliminaries1. Molecular biology and high-throughput sequencing2. Algorithm design3. Data structures4. Graphs5. Network flowsPart II. Fundamentals of Biological Sequence Analysis6. Alignments7. Hidden Markov models (HMMs)Part III. Genome-Scale Index Structures8. Classical indexes9. Burrows–Wheeler indexesPart IV. Genome-Scale Algorithms10. Read alignment11. Genome analysis and comparison12. Genome compression13. Fragment assemblyPart V. Applications14. Genomics15. Transcriptomics16. MetagenomicsReferencesIndex.

 

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