ArticleScientific reports2023
Machine learning for design of degenerate Cas13a crRNAs using lassa virus as a model of highly variable RNA target.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- On-site and visual detection of genotype VII Newcastle disease virus based on RT-RPA and CRISPR/Cas13a.Frontiers in veterinary science · 2026Article
- Detection of Murine Norovirus on Fresh Produce Through a CRISPR/Cas13a RNase-Based Capsid Integrity Assay.Food and environmental virology · 2025Article
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7 authors.
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Abstract
The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algorithm (RuleFit) was applied to define the top attributes that determine the specificity of degenerate crRNAs to elicit collateral nuclease activity. Although the total number of mismatches (0-4) is important, the specificity depends as well on the spacing of mismatches, and their proximity to the 5' end of the spacer. We developed a predictive algorithm for design of candidate degenerate crRNA sets, allowing improved discrimination between "included" and "excluded" groups of related target sequences. A single degenerate crRNA set adhering to these rules detected representatives of all Lassa lineages. Our general ML approach may be applied to the design of degenerate crRNA sets for any CRISPR/Cas system.
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