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3 - Data structures

from Part I - Preliminaries

Published online by Cambridge University Press:  28 September 2023

Veli Mäkinen ,
Djamal Belazzougui ,
Fabio Cunial  and
Alexandru I. Tomescu
Veli Mäkinen
Affiliation:
University of Helsinki
Djamal Belazzougui
Affiliation:
Centre de Recherche sur l’Information Scientifique et Technique (CERIST), Algiers
Fabio Cunial
Affiliation:
Broad Institute, Massachusetts
Alexandru I. Tomescu
Affiliation:
University of Helsinki
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Summary

This chapter presents the minimal setup of data structures required to follow the rest of the book in a self-contained manner. Balanced binary trees are enhanced to solve dynamic range minimum queries. Bitvector rank and select data structures and their extensions to larger alphabets with wavelet tree are covered. Then a special structure for solving static range minimum queries is derived. The chapter ends with a concise description of hashing primitives, such as perfect hashing, Bloom filters, minimizers, and the Rabin–Karp rolling hash.

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Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
 , pp. 21 - 41
Publisher: Cambridge University Press
Print publication year: 2023

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