Computational Tool Choice Impacts CRISPR Spacer-Proto spacer Detection
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ID: 319066
2026
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Abstract
Abstract Motivation CRISPR 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. Results Using 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) Supplementary information Supplementary data are available at Bioinformatics online.
| Reference Key |
openalex_W7166574566
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|---|---|
| Authors | Uri Neri, Antônio Pedro Camargo, Brian Bushnell, Rick Beeloo, Simon Roux |
| Journal | BMC Bioinformatics |
| Year | 2026 |
| DOI |
10.1093/bioinformatics/btag394
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| URL | |
| Keywords | Keywords not found |
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