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8 - Classical indexes

from Part III - Genome-Scale Index Structures

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

A full-text index for a string T is a data structure that is built once and that is kept in memory for answering an arbitrarily large number of queries on the position and frequency of substrings of T. Such queries can be used for speeding-up dynamic programming algorithms tailored for mapping reads to a reference genome – a fundamental task in the analysis of high-throughput sequencing data. This chapter covers the classical full-text indexes and the like, including k-mer indexes, suffix arrays, and suffix trees. Linear-time algorithms for suffix sorting and for basic genome analysis tasks, such as finding maximal exact matches, are also presented.

Type
Chapter
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Genome-Scale Algorithm Design
Bioinformatics in the Era of High-Throughput Sequencing
 , pp. 145 - 173
Publisher: Cambridge University Press
Print publication year: 2023

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