Replacing suffix trees with enhanced suffix arrays

The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every a...

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Bibliographic Details
Published in:Journal of discrete algorithms (Amsterdam, Netherlands) Vol. 2; no. 1; pp. 53 - 86
Main Authors: Abouelhoda, Mohamed Ibrahim, Kurtz, Stefan, Ohlebusch, Enno
Format: Journal Article
Language:English
Published: Elsevier B.V 2004
Subjects:
Genome comparison
Pattern matching
Repeat analysis
Suffix array
Suffix tree
Suffix tree
Suffix array
Genome comparison
Pattern matching
Repeat analysis
ISSN:1570-8667, 1570-8675
Online Access:Get full text
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Summary:The suffix tree is one of the most important data structures in string processing and comparative genomics. However, the space consumption of the suffix tree is a bottleneck in large scale applications such as genome analysis. In this article, we will overcome this obstacle. We will show how every algorithm that uses a suffix tree as data structure can systematically be replaced with an algorithm that uses an enhanced suffix array and solves the same problem in the same time complexity. The generic name enhanced suffix array stands for data structures consisting of the suffix array and additional tables. Our new algorithms are not only more space efficient than previous ones, but they are also faster and easier to implement.
ISSN:1570-8667
1570-8675
DOI:10.1016/S1570-8667(03)00065-0