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

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 Di...

Full description

Saved in:
Bibliographic Details
Published inBriefings in bioinformatics Vol. 15; no. 2; pp. 138 - 154
Main Authors Shrestha, A. M. S., Frith, M. C., Horton, P.
Format Journal Article
LanguageEnglish
Published England Oxford Publishing Limited (England) 01.03.2014
Oxford University Press
Subjects
Algorithms
Bioinformatics
Computational Biology - methods
Databases, Nucleic Acid - statistics & numerical data
Grammar
Humans
Pattern Recognition, Automated - statistics & numerical data
Software
subset seeds
text index
spaced seeds
suffix array construction
linear-time algorithm
Online AccessGet full text
ISSN1467-5463
1477-4054
1477-4054
DOI10.1093/bib/bbt081

Cover

More Information
Summary: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.
Bibliography:SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 14
ObjectType-Article-1
ObjectType-Feature-2
content type line 23
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbt081