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An Elegant Algorithm for the Construction of Suffix Arrays.

Sanguthevar Rajasekaran1, Marius Nicolae1

  • 1Dept. of Computer Science and Engineering, Univ. of Connecticut, Storrs, CT, USA.

Journal of Discrete Algorithms (Amsterdam, Netherlands)
|July 22, 2014
PubMed
Summary

We introduce a new, simple, and efficient algorithm for suffix array construction that runs in linear time with high probability. This algorithm is easily parallelizable and offers significant speedups for string processing tasks.

Keywords:
high probability boundsparallel algorithmsuffix array construction algorithm

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Area of Science:

  • Computer Science
  • Bioinformatics
  • Data Structures

Background:

  • Suffix arrays are crucial data structures for string processing in diverse fields.
  • Existing suffix array construction algorithms (SACAs) have limitations in practical efficiency.
  • There is a need for faster and more efficient SACAs.

Purpose of the Study:

  • To present a novel, elegant, and efficient algorithm for suffix array construction.
  • To develop a parallelizable algorithm for suffix array construction.
  • To introduce RadixSA, an algorithm with improved worst-case runtime.

Main Methods:

  • Developed a new linear-time suffix array construction algorithm (SACA) with high probability.
  • Proved a lemma on ℓ-mers of random strings for potential independent applications.
  • Introduced RadixSA, an algorithm utilizing the new SACA, with O(n log n) worst-case runtime.

Main Results:

  • The new SACA is one of the simplest known and offers a new approach to construction.
  • The algorithm is easily parallelizable, with implementations on various parallel models.
  • RadixSA demonstrates competitive performance, ranking among the fastest algorithms in empirical comparisons.

Conclusions:

  • The presented algorithm offers a theoretically sound and practically efficient solution for suffix array construction.
  • The RadixSA algorithm and its underlying techniques have the potential to accelerate other SACAs.
  • The freely available C++ source code facilitates adoption and further research.