Faster computation of left-bounded shortest unique substrings

Finding shortest unique substrings (SUS) is a fundamental problem in string processing with applications in bioinformatics. In this paper, we present an algorithm for solving a variant of the SUS problem, the left-bounded shortest unique substrings (LSUS). This variant is particularly important in a...

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Bibliographic Details
Published in:Algorithms for molecular biology Vol. 20; no. 1; pp. 11 - 7
Main Authors: Aguiar, Larissa L. M., Louza, Felipe A.
Format: Journal Article
Language:English
Published: London BioMed Central 20.06.2025
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Arrays
Bioinformatics
Biomedical and Life Sciences
Cellular and Medical Topics
Compact data structures
Computational Biology/Bioinformatics
Data compression
Extraction
Genomes
Grammar
Life Sciences
Numbers
Physiological
Strings
Extraction
Algorithms
Grammar
Data compression
Compact data structures
ISSN:1748-7188, 1748-7188
Online Access:Get full text
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Summary:Finding shortest unique substrings (SUS) is a fundamental problem in string processing with applications in bioinformatics. In this paper, we present an algorithm for solving a variant of the SUS problem, the left-bounded shortest unique substrings (LSUS). This variant is particularly important in applications such as PCR primer design. Our algorithm runs in O ( n ) time using 2 n memory words plus n bytes for an input string of length n . Experimental results with real and artificial datasets show that our algorithm is the fastest alternative in practice, being two times faster (on the average) than related works, while using a similar peak memory footprint.
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ISSN:1748-7188
1748-7188
DOI:10.1186/s13015-025-00287-5