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bioRxiv · 10.1101/2025.11.25.690584

Efficient Identification of Short Tandem Repeats via Context-Aware Motif Discovery and Ultra-Fast Sequence Alignment

Liao, X.·Wen, L.·Jing, M.·Li, X.·Chen, B.·Zhang, B.·Gao, X.·Shang, X.
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Abstract

Tandem repeats (TRs) are highly polymorphic genomic elements, associated with diverse molecular traits and implicated in numerous human diseases. However, large-scale analysis of TRs has been limited by computational challenges, including motif recognition, detection in complex regions, and excessive computational cost. Here we present FastSTR, a computationally efficient tool for precise detection and characterization of TRs. FastSTR integrates a context-aware N-gram motif model with a segmented global alignment algorithm to enable accurate motif identification and boundary definition, even for repeat units up to 8 bp. Across 13 species, FastSTR achieved >90% recall and 99% precision, running several times faster than existing methods white outperforming them in both sensitivity and accuracy. Applied to the human genome, FastSTR uncovered previously unannotated HSATII elements, resolved population-specific TR demonstrate, and identified recurrent STR alterations in lung cancer. These results demonstrate FastSTR as a versatile framework for TR annotation and discovery, advancing studies of genome evolution, genetic diversity, and disease.

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Liao, X., Wen, L., Jing, M., Li, X., Chen, B., Zhang, B., Gao, X., Shang, X.. 2025-11-28. Efficient Identification of Short Tandem Repeats via Context-Aware Motif Discovery and Ultra-Fast Sequence Alignment. https://doi.org/10.1101/2025.11.25.690584

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