CRISPR/Cas9 single guide RNA design software tools | Genome engineering data analysis
The Type II clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system is an adaptive immune response in prokaryotes, protecting host cells against invading phages or plasmids by cleaving these foreign DNA species in a targeted manner. CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) enable genome editing in cultured cells, animals and plants, but are limited by off-target mutations.
Scans a DNA sequence for identifying potential zinc finger protein (ZFP) and zinc finger nuclease (ZFN) binding sites. ZiFiT is a web server that enables customizable searches for potential ZFP and ZFN-binding sites that can be targeted using either the modular assembly or OPEN engineering methods. The software also provides several tools to assist the evaluation of ZFP targets, such validated scoring schemes for ranking potential target sites, or a tool for querying NCBI BLAST servers for potential off-target sites.
A web tool crafted to simplify the process of CRISPR guide selection in an input DNA sequence by (i) discovering possible offtargets genome-wide, (ii) highlighting guides with high target specificity, and (iii) flagging guides with numerous or genic offtargets in target genomes. The CRISPR design tool allows users to enter a 23-1000bp DNA sequence of interest and will find all SpCas9 target sites within the input sequence. The result will contain a rank ordered list of target sites based on predicted specificity.
A web tool for CRISPR- and TALEN-based genome editing. The overarching principle of CHOPCHOP is to provide an intuitive and powerful tool that can serve first time as well as experienced users. The basic mode offers optimized defaults for the basic user, while more advanced users can select from a wide range of options curated from the literature by their relevance and utility. All options are presented in a tabulated and organized manner to help users quickly visualize and evaluate options when designing CRISPR experiments.
Consists of a web server for selecting rational CRISPR/Cas targets from an input sequence. CRISPRdirect enables selection of rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. It is able to investigate the entire genome for perfect matches with each candidate target sequence. Users can also browse the detailed list of potential off-target sites that have partial complementarity with the selected sequence.
A web tools for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences, including screenable markers.