Plant CRISPR Search Tool

For gRNA search paste your target region in BED format into the box (example). Target region is defined by TABs delimited chromosome name, start and end position and optionally a target name. Alternatively, you can use the JBrowse for graphical selection of the target region.

Select genome from the list:

Options

Design settings

Upstream search region (bp): Downstream search region (bp):

Upstream exclude region (bp): Downstream exclude region (bp):

Off-target settings

Off-targets:

off0	off1	off2	off3	off4

gRNA scoring

Minimum individual score:

Minimum paired score:

Score combination: SumProduct

Output

Number of gRNAs per target: Ranking method:

Diversity:

If design settings are OK, please click 'submit job'


Upstream design region	It corresponds to the region where the system will search for gRNAs upstream the provided 'target region'. Its value represents the length in base pairs (bp).
Downstream design region	It corresponds to the region where the system will search for gRNAs downstream the provided 'target region'. Its value represents the length in base pairs (bp).
Upstream exclude region	It corresponds to the upstream region adjacent to the target that will be excluded for gRNAs search. The value represents length in base pairs (bp).
Downstream exclude region	It corresponds to the downstream region adjacent to the target that will be excluded for gRNAs search. The value represents length in base pairs (bp).

The selection of each gRNA is based on an empirical efficiency score, estimated by the logistic regression measure of Doench et al. (2014). This model predicts gRNA efficiency based on nucleotide preferences within the protospacer region and also considers some flanking nucleotides. For gRNA pairs selection, a combined score is considered, which is by default the addition of two individual gRNA scores.


Individual score	The minimum individual efficiency score for each gRNA. The efficiency score takes values between 0 and 1 (0.2 by default).
Paired score	The minimum combined score for a selected gRNA pair (0.4 by default).
Score combination	Method for gRNA pair scoring. Individual scores can be combined by addition (default) or multiplication.

Number of gRNAs per target

The maximum number of gRNA pairs to be returned

Ranking method

There are two criteria for gRNA pairs ranking:

Score:	The gRNA pairs will be ordered by descending paired score (default)
Distance:	The gRNA pairs will be ordered by ascending distance between both protospacers

Diversity

In theory, a single high scored gRNA can be combined with many others to form high-scored pairs. Diversity controls the maximum fraction of returned pairs that contain the same gRNA (0.5 by default)