ArticleBioinformatics (Oxford, England)2026
Computational tool choice impacts CRISPR spacer-protospacer detection.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 authors.
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Abstract
motivationCRISPR spacer-protospacer matching is widely used to infer host-virus interactions in microbial and viromics studies, but the choice of sequence search or alignment tool and its reporting behavior is often under-evaluated for this specific task.
resultsUsing synthetic, semi-synthetic, and real datasets, we benchmarked commonly used tools and observed substantial differences in recall, runtime, and resource usage across distance metrics and thresholds. Our analyses support practical defaults for large-scale spacer-target matching and clarify trade-offs between exhaustive and heuristic approaches. AVAILABILITY: Source code and benchmark workflows are available at https://github.com/UriNeri/spacer_matching_bench. Data and run artifacts are archived on Zenodo (https://doi.org/10.5281/zenodo.15171878).
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