A bioinformatician's guide to the forefront of suffix array construction algorithms

Anish Man Singh Shrestha, Martin C. Frith, Paul Horton

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

The suffix array and its variants are text-indexing data structures that have become indispensable in the field of bioinformatics. With the uninitiated in mind, we provide an accessible exposition of the SA-IS algorithm, which is the state of the art in suffix array construction.We also describe DisLex, a technique that allows standard suffix array construction algorithms to create modified suffix arrays designed to enable a simple form of inexact matching needed to support 'spaced seeds' and 'subset seeds' used in many biological applications.

Original languageEnglish
Article numberbbt081
Pages (from-to)138-154
Number of pages17
JournalBriefings in bioinformatics
Volume15
Issue number2
DOIs
Publication statusPublished - 2014 Mar

All Science Journal Classification (ASJC) codes

  • Information Systems
  • Molecular Biology

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