is a rational and flexible tool for finding Cas9 target sites with low/no off-targeting potential. Given a DNA query (eg. Gene) sequence, the pipeline first fetches all the possible regions of length 23, structured as [5p- G(19bps)NGG -3p]. Further these regions are evaluated and filtered to show low/no off-target activity across the whole genome.
There are two levels of filters, passing both designates the region a potential sgRNA for Cas9 activity. The first level rejects the target and tag it "FAIL" if it has more than 2 matches with the off-targets in the genome and second filter, which runs in parallel, rejects the target if the seed region (last 15 bases including the PAM sequence) has 100% match with the off-targets anywhere in the genome. The pipeline reports only the instances which are accepted by both the filters and are designated as potential Cas9 targets.
pipeline is mounted with the index of 13 Protist genomes and is accessible via web-server. An off-line standalone software is also developed which gives liberty to its users to use it for any genome, assembled or un-assembled.
We always work on improvements in our programs, to make them better, smarter and user friendly. Thus, feel free to post valuable suggestions, bugs or troubleshooting queries via email at
Institut de Biologie de l'ENS (IBENS)