Guide RNA design for CRISPRi in bacteria

Input the sequence of a target gene and this script will output candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity and an analysis of off-targets. Predictions are made based on a model of dCas9's ability to block the RNA polymerase of E. coli (Calvo-Villamañán et al., 2020) .

1. Paste the sequence of your target gene (can include the 5'UTR). The gene sequence needs to be in the positive orientation (start on the left)

Example

The sequence is valid !

A valid sequence contains only ATGC

2. Optional: upload a genome to obtain an analysis of off-targets

Example (Escherichia coli str. K-12 substr. MG1655)

Choose sequence format

Choose sequence file