Commonly used CRISPR Tools
A CRISPR experiment involves an elaborate process. It requires computerised software and bioinformatics tools that help in designing the appropriate sgRNA capable of guiding the Cas9 nuclease to the target DNA site for the desired gene editing. Prior to the experiment, the CRISPR/Cas tools are selected based on the requirements of the experiment and the potential off-target effect of the designed sgRNA depending upon the tools used.
Some of the commonly used CRISPR/Cas tools are:
1) Name: Invitrogen TrueDesign Genome Editor
Provider: Thermo Fisher Scientific
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 3
Does it predict the activity of the sgRNA: No
Website:https://www.thermofisher.com/in/en/home/life-science/genome-editing/geneart-crispr/geneart-crispr-search-and-design-tool.html
Description: The free CRISPR/Cas design tool has an intuitive ‘point-and-type interface’ that allows to generate whole knock-in design and to edit up to 30 bases in human genes flexibly and within a short span of time. Users can easily find the transcript and loci of interest by navigating the human genome. It also allows adding marker tags such as GFP and luciferase and creating adaptor primers.
2) Name: Cas-OFFinder
Provider: Seoul National University
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 10
Does it predict the activity of the sgRNA: No
Website: http://www.rgenome.net/cas-offinder/
Description: It is an algorithm that identifies potential off-target sites of Cas9 RNA-guided endonucleases within the target genome or user-defined genomic sequences. The Cas-OFFindertoolis known to be fast and versatile.
3) Name: Breaking-Cas
Provider: Spanish National Center for Biotechnology
Does it search the entire genome for a suitable target: Yes (over 1000 genomes)
Maximum number of mismatch supported: 4
Does it predict the activity of the sgRNA: No
Website: https://bioinfogp.cnb.csic.es/tools/breakingcas/
Description: This tool allows the interactive design of sgRNA for ENSEMBL genomes. Unlike most CRISPR/Cas tools, this tool allows the use of all eukaryotic genomes in the ENSEMBL to set the sgRNA length and score per nt by using different PAM sequences at 5ʹ or 3ʹ end.
4) Name: CRISPy
Provider: Technical University of Denmark
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: All
Does it predict the activity of the sgRNA: No
Website: https://crispy.secondarymetabolites.org/
Description: The simple web-based tool allows designing sgRNA for any user-defined microbial genome. It interactively allows users to select and scan the region of the microbial genome for possible sgRNA designing. The resulting sgRNA is displayed graphically after assessing potential off-target effects, and the designed sgRNA can be exported to text files.
5) Name: CRISPR Targeted Gene Designer
Provider: Horizon Discovery
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 4
Does it predict the activity of the sgRNA: Yes
Website: https://horizondiscovery.com/en/ordering-and-calculation-tools/crispr-targeted-gene-designer
Description: The web-based tool offers an interactive input platform to design sgRNA for targeted gene knock-out or site-specific HDR editing. It assists in designing sgRNA for any editing nuclease in over 40 species capable of targeting coding, non-coding, or microRNAs.
6) Name: CCTop
Provider: University of Heidelberg
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 5
Does it predict the activity of the sgRNA: Yes
Website: https://cctop.cos.uni-heidelberg.de:8043/
Description: It is a standalone CRISPR/Cas9 target online predictor. It offers an intuitive user interface and uses parameters that can be easily tuned as per the requirements. The tool identifies target sites for the designed sgRNA and based on off-target effects, ranks them.
7) Name: CHOPCHOP
Provider: Harvard University
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0, 2
Does it predict the activity of the sgRNA: No
Website: https://chopchop.cbu.uib.no/
Description: The tool allows rapid designing of sgRNA. The tool accepts inputs such as gene identifiers, genomic regions, or pasted genomic sequences and offers an array of options for selecting the target. The tool uses efficient sequence alignment algorithms to assess potential off-target binding sites of the sgRNA and offers visualisation of the binding interactions of the sgRNA with target sites.
8) Name: CHOPCHOP v2
Provider: University of Bergen
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 3
Does it predict the activity of the sgRNA: Yes
Website: http://chopchop.cbu.uib.no/
Description: CHOPCHOPv2 is an improvement over the CHOPCHOP CRISPR/Cas9 tool. In addition to existing features in the CHOPCHOP tool, the CHOPCHOPv2 can scan for the self-complementarity of the sgRNA to identify possibilities of internal interactions that can lower the efficiency of the sgRNA-Cas9 complex to cleave the target genome.
9) Name: CRISPOR
Provider: University of California, Santa Cruz TEFOR
Does it search the entire genome for a suitable target: Yes (over 200 genomes)
Maximum number of mismatch supported: 4
Does it predict the activity of the sgRNA: Yes
Website: http://crispor.tefor.net/
Description: The intuitive guide selection web-based tool allows designing, assessing, and cloning sgRNA sequences for CRISPR/cas9 experiments. The user is required to provide DNA sequence and genome as input in FASTA format. The tool uses algorithms to predict off-target and on-target scores.
10) Name: CRISPR Design
Provider: Zhang Lab, MIT
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 4
Does it predict the activity of the sgRNA: No
Website: https://horizondiscovery.com/en/ordering-and-calculation-tools/crispr-design-tool
Description: The web-based tool allows intuitive designing of sgRNA for targeted gene knock-out or specific HDR-mediated gene editing for any editing nuclease. The user can choose different sgRNA formats such as synthetic, lentivirus, or all-in-one.
11) Name: CRISPRdirect
Provider: Database Center for Life Science
Does it search the entire genome for a suitable target: Yes (over 200 species)
Maximum number of mismatch supported: Any number
Does it predict the activity of the sgRNA: No
Website: https://crispr.dbcls.jp/
Description: The simple and functional web server allows selecting CRISPR/Cas9 targets and rationalised designing of sgRNA with reduced potential off-target effects for CRISPR/Cas technique.
12) Name: CRISPRscan
Provider: Giraldez Lab, Yale
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 4
Does it predict the activity of the sgRNA: Yes
Website: https://www.crisprscan.org/
Description: The web-based tool allows to search for sgRNAs on genes and to predict the sgRNA for the chosen genome and potential off-target effects. Using the novel scoring algorithm, the CRISPRscan tool helps to select the best sgRNAs for the experiment.
13) Name: CRISPRseek
Provider: Bioconductor
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: Any number
Does it predict the activity of the sgRNA: No
Website: http://bioconductor.org/packages/release/bioc/html/CRISPRseek.html
Description: It is a flexible and open-sourced software package that helps to identify sgRNA while reducing the potential off-target interactions.
14) Name: DESKGEN
Provider: Desktop Genetics
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: Any number
Does it predict the activity of the sgRNA: Yes
Website: https://www.deskgen.com/landing/
Description: DESKGEN is a free curated cloud platform. It uses algorithms and uses multiple experiment-focused designs setting for sgRNA design, and uses a modern approach to improve precision rate via the HDR pathway. DESKGEN can help to design CRISPR libraries with off-target scores for precise genome editing.
15) Name: GuideScan
Provider: GuideScan
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 3 (website), but can be customised.
Does it predict the activity of the sgRNA: Yes
Website: http://www.guidescan.com/
Description: The web-based tool assists in designing high specific sgRNA for editing both coding and noncoding genomic sequences. The tool produces high-density sets of sgRNA for genome-wide screens.
16) Name: GT-Scan
Provider: CSIRO & EMBL-ABR
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 3
Does it predict the activity of the sgRNA: No
Website: https://gt-scan.csiro.au/
Description: The GT-scan is a flexible web-based tool that searches potential targets with minimum risk of off-targets within the genomic region selected by the user and ranks these targets based on their potential off-target effects. Based on the advanced learning model, GT-scan can also score potential targets based on predicted incision efficiency obtained from genetic and epigenetic knowledge.
17) Name: Off-Spotter
Provider: Thomas Jefferson University
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 5
Does it predict the activity of the sgRNA: No
Website: https://cm.jefferson.edu/Off-Spotter/
Description: It is a rapid and flexible web-based tool that allows sgRNA designing using different choices of PAM and based on the number of mismatches allowed. The output is flexible and allows results to be viewed by hiding/viewing columns as needed.
18) Name: sgRNA Designer
Provider: Broad Institute
Does it search the entire genome for a suitable target: No
Maximum number of mismatch supported: 0
Does it predict the activity of the sgRNA: Yes
Website: https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design
Description: The web-based tool designs sgRNA for CRISPRi/CRSIPRa based on the sgRNA targets and ranks the sgRNA sequences based on their on-target and off-target scores.
19) Name: Synthego Design Tool
Provider: Synthego
Does it search the entire genome for a suitable target: Yes (over 120,000 genomes)
Maximum number of mismatch supported: 3
Does it predict the activity of the sgRNA: Yes
Website: https://design.synthego.com/#/
Description: The free web-based tool can help to design sgRNA to target over 120,000 genomes and almost immediately identifies sgRNA sequences capable of targeting a gene based on multiple algorithms. It also predicts the sgRNA that is likely to have high efficiency and low-target effects.
20) Name: VARSCOT
Provider: BauerLab
Does it search the entire genome for a suitable target: Yes
Maximum number of mismatch supported: 0 to 8
Does it predict the activity of the sgRNA: Yes
Website: https://github.com/BauerLab/VARSCOT
Description: In contrast to other CRISPR tools, VARSCOT allows up to 8 mismatches that can be found in experimental data. Also, VARSCOT considers genetic variations such as SNPs and INDELs, unlike other pipelines that can alter the off-target events. These make VARSCOT a suitable tool for designing sgRNAs for personalised and advanced applications such as gene therapy and gene drives.