DIGGER-Bac: prediction of seed regions for high-fidelity construction of 
synthetic small RNAs in bacteria

Philipp, N.; Brinkmann, C. K.; Georg, J.; Schindler, D.; Berghoff, B. A.

doi:10.1093/bioinformatics/btad285

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DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria

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Brinkmann, C. K.
Core Facility MPG MAXGenesys DNAfoundry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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Schindler, D.
Core Facility MPG MAXGenesys DNAfoundry, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;

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https://doi.org/10.1093/bioinformatics/btad285
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Citation

Philipp, N., Brinkmann, C. K., Georg, J., Schindler, D., & Berghoff, B. A. (2023). DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. Bioinformatics, 39(5): btad285. doi:10.1093/bioinformatics/btad285.

Cite as: https://hdl.handle.net/21.11116/0000-000D-06A0-7

Abstract

SUMMARY: Synthetic small RNAs are gaining increasing attention in the field of synthetic biology and bioengineering for efficient post-transcriptional regulation of gene expression. However, the optimal design of synthetic small RNAs is challenging because alterations may impair functions or off-target effects can arise. Here, we introduce DIGGER-Bac, a toolbox for Design and Identification of seed regions for Golden Gate assembly and Expression of synthetic small RNAs in Bacteria. The SEEDling tool predicts optimal small RNA seed regions in combination with user-defined small RNA scaffolds for efficient regulation of specified mRNA targets. Results are passed on to the G-GArden tool, which assists with primer design for high-fidelity Golden Gate assembly of the desired synthetic small RNA constructs. AVAILABILITY AND IMPLEMENTATION: Both SEEDling and G-GArden are freely available at https://github.com/DIGGER-Bac under the CC BY-NC-SA 4.0 license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.