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Fast, parallel, and cache-friendly suffix array construction.

Jamshed Khan1, Tobias Rubel2, Erin Molloy2

  • 1Department of Computer Science, University of Maryland, College Park, MD, 20742, USA. jamshed@cs.umd.edu.

Algorithms for Molecular Biology : AMB
|April 28, 2024
PubMed
Summary
This summary is machine-generated.

We developed CAPS-SA, a parallel algorithm for constructing suffix arrays (SA) and longest common prefix (LCP) arrays. This simple, scalable method offers superior performance on modern hardware.

Keywords:
Data structuresIndexingLongest common prefixParallel algorithmsSuffix array

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • String Algorithms

Background:

  • Suffix arrays (SA) and longest common prefix (LCP) arrays are crucial for bioinformatics.
  • Scalable parallel algorithms for constructing SA and LCP arrays are limited and complex.
  • Existing methods face implementation and parallelization challenges.

Purpose of the Study:

  • To present CAPS-SA, a novel, simple, and scalable parallel algorithm for SA and LCP array construction.
  • To improve the efficiency and performance of string index generation on modern multicore systems.
  • To introduce and leverage bounded-context suffix arrays for specific applications.

Main Methods:

  • CAPS-SA is inspired by samplesort and uses an LCP-informed mergesort.
  • The algorithm is designed for excellent memory locality, reducing cache misses.
  • It is easily extendable to exploit bounded-context suffix array structures.

Main Results:

  • CAPS-SA demonstrates superior performance compared to state-of-the-art parallel SA/LCP construction algorithms.
  • The algorithm achieves strong performance on modern multicore architectures.
  • Extension for bounded-context SA yields further speedups.

Conclusions:

  • CAPS-SA offers a simple yet highly effective solution for parallel string index construction.
  • The algorithm's performance and scalability make it suitable for demanding bioinformatics tasks.
  • Public availability of the code facilitates adoption and further research.