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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Published inAlgorithms for molecular biology Vol. 20; no. 1; pp. 11 - 7
Main Authors Aguiar, Larissa L. M., Louza, Felipe A.
Format Journal Article
LanguageEnglish
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
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ISSN1748-7188
1748-7188
DOI10.1186/s13015-025-00287-5

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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