Current features (beta)
- Works on common operating systems. Executable binaries available for Mac OS X and Windows.
- Tabulates Cas9 (NGG) target sites for any small to medium sized genome of interest.
- Pre-calculated databases for several organisms.
- Browse a genome's repertoire of Cas9 target-sites quickly.
- Sub-select target sites based on distance from a point (e.g. the stop coordinate of a gene).
- Sub-select target sites between two genomic coordinates.
- Sub-select target sites within a gene.
- Filter targets by the type of PAM motif (NGG, or NAG).
- Filter targets by annotation: 'genic', 'intergenic', 'exonic', 'intronic', and 'UTR'.
- Filter targets by their degree of uniqueness.
- Sort targets by any information, in descending or ascending order.
- Thoroughly compare a guide-RNA sequence to all potential sites in a genome.
- Rank off-target comparisons by the number of mismatches or a likelihood score.
- Likelihood scores are calculated by an adapted version of this algorithm, developed from results by Hsu et al, Nature Biotechnology 2013.
- Identify all NGG/NAG sites in custom sequences less than 100,000 nt long.
- Connect to and control the Integrative Genomics Viewer (IGV) for even more powerful analyses (observe local annotations, visualise target-sites in the context of any high-throughput sequencing data, view amino acid translations useful for the shield technique mentioned here). This was made possible from code developed by Brent Pedersen and made available on github.
- Progress bar during CPU intensive calculations.
- Optimized data model (HDF5) and searching algorithms.
- Fast indexing of large genomes.
- Easily create your own database for any small to medium sized genome (already possible, just not easy).
- Share your custom database with the community and/or collaborators.
- GFF parser for the PDC - Protospacer Database Creator.
- Mark targets of interest and rank them according to predicted off-target activity.
- Scripting access through Python version 2.x for large or complicated tasks.
- Database summary tab and capability to store meta-information.
- System requirements (database dependant).
- Named searches for easier history tracking.
- Save and load workflows / history.
- Annotation and ID search engine allowing multiple nomenclatures (currently, genes are only allowed one ID).
- Anchored search for optimized gRNA-pair design.
- Plotting and report generation.