GBSC: Graph-Based Sequence Clustering method for similar short tandem repeats in protein sequences

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ID: 317404
2026
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Abstract
MOTIVATION: Short tandem repeats (STRs) are abundant in protein sequences and play an important role in determining their structures and functions. Strikingly, the unusual compositional characteristics of tandem repeats break classical sequence analysis tools. RESULTS: We here establish the first algorithm to effectively identify and cluster STRs: Graph-Based Sequence Clustering (GBSC) features linear time complexity, and clusters protein sequence fragments based on their STRs, while allowing for insertions and mutations, supporting an analysis of imperfect or cryptic repeats. Due to its computational efficacy, our algorithm can be used to systematically scan for patterns in large datasets. We compare our method both with state-of-the-art methods for identifying STRs in proteins and alternative clustering approaches. Unlike existing STR analysis methods, GBSC clusters repeat patterns rather than raw sequences, operating at the level of structural repeat identity, while tolerating biological variations and preventing erroneous merging of structurally and functionally distinct motifs. Whereas functional annotation is typically only available at the protein level, the functions of individual STRs and sequences of adjacent STRs remains largely unknown. On a challenging use-case we here demonstrate and discuss how our method can be used to associate previously unannotated repetitive protein fragments with similar ones, allowing a transfer of annotation by similarity. For the first time, GBSC offers a tool that systematically extends this fundamental bioinformatics principle to low-complexity regions across large datasets. AVAILABILITY AND IMPLEMENTATION: GBSC is available at GitHub https://github.com/patryk-jarnot/GBSC and https://doi.org/10.5281/zenodo.18965247. The data and scripts to reproduce the analysis are available at https://doi.org/10.5281/zenodo.16906653.
Reference Key
openalex_W7164839278 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Patryk Jarnot, Joanna Ziemska-Legięcka, Marcin Grynberg, Vasilis J. Promponas, Aleksandra Gruca
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag378
URL
https://doi.org/10.1093/bioinformatics/btag378
Keywords Keywords not found

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