A bioinformatician's guide to the forefront of suffix array construction algorithms.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 24413184.
- Also identified by DOI 10.1093/bib/bbt081 and PMC identifier 3956071.
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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.
Medical subject headings
- Algorithms
- Computational Biology