I read an article in which scientists design short and long fragments for a gene which contains an inverted repeat of gene for RNAi-mediated gene silencing in bacteria. But in the article and its reference article -experimenting with fungi- do not give any information about how to design such fragments. I will perform prokaryotic RNAi. Does anybody know any design tools for RNAi in bacteria?
Check this link whether they have anything for prokaryotes.
https://www.dkfz.de/signaling/e-rnai3/
RNAi is a eukaryotic type of regulation, it is possible to perform a similar type of RNA-based regulation in prokaryotes but its not quite the same as RNAi (due to lack of the rest of the RNAi machinery)
These papers may help
Prokaryotic RNAi | Nature Methods
Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs - ScienceDirect
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