How to Use CRISPR-GATE

FAQs

1. How to browse for tools?

Step 1

The Tools page can be directly accessed by clicking on the 'TOOLS' menu (1) from any page, otherwise the Home page provides 'Explore Tools' button (4). The 'HOW TO USE' menu (2) provides a detailed guide to make use of the resource. Further, the 'USER SUGGESTIONS' menu (3) allows users to submit relevant tools to the resource, which our team will review and add upon validation.

Step 2

From the Tools page, choose required 'Tool Category' (1), 'Tool Subcategory' (2) if available and the 'Filter' (3) option accordingly. Finally, click on the 'Search' button (4) to obtain the results.

Step 3

Look for the best and apt tool after examining 'Feature Wise Comparison' plot (1), 'Key Features' (2) and 'Limitations' (3). Direct link to the tool (4) and reference (5) are provided. Set the number of rows per view (6) and browse every page accordingly. Find field (7) can also be utilized for searching specific keywords.

2.What are the different categories and filter options available?

Available 'Tool Category' options and their corresponding 'Tool Subcategory' options are given in the table below.
Tool Category Tool Subcategory
All tools Not available
CRISPR-Cas systems All tools
CRISPR arrays
Cas proteins
CRISPR-Cas systems
PAM
anti-CRISPR proteins
Canonical gRNA Design All tools
Alignment- & Hypothesis-based
Learning-based
Cas9 mutation prediction Not available
Base editing All tools
Design
Outcome prediction
Prime editing All tools
Design
Outcome prediction
Plant experiments Not available
Analysis and visualization All tools
Multipurpose
Canonical experiments
CRISPR Screens
Base editing
Prime editing

Available 'Filter' options for all the categories include:

All Tools
Web Tools
Standalone Tools

Note: Some tools provide both web interface and standalone tool. However, we have only provided the link to web tool when both are available.

3.What kind of tools does each category provide?

All Tools

It includes the list of tools falling under every category that aids in the CRISPR-Cas experiments, starting from the discovery of CRISPR-Cas systems to the final downstream analysis of those experiments.

CRISPR-Cas systems -> All tools

The list comprises various tools which aids in the discovery of CRISPR-Cas systems, those that explore CRISPR arrays and Cas genes separately or together. It also covers tools devoted to metagenomic datasets and tools that facilitate the identification of PAM sequences.

CRISPR-Cas systems -> CRISPR arrays

An assortment of tools is included in the list, that are dedicatedly developed for the discovery of CRISPR arrays which consist of repeat sequences and unique spacer sequences. The CRISPR arrays upon transcription finally mature into various mature small crRNAs.

CRISPR-Cas systems -> Cas proteins

It includes those tools that explore the presence of Cas genes or Cas proteins which are crucial to the success of CRISPR-Cas experiments. Cas proteins contain the cleavage domains for making desired edits.

CRISPR-Cas systems -> CRISPR-Cas systems

Within the list, you will find a compilation of tools that simultaneously support the CRISPR array and Cas gene identification and characterization. This helps to avoid the need for separate searches and makes it easier.

CRISPR-Cas systems -> PAM

It includes those tools that facilitate the identification of brief as well as conserved PAM sequences. The occurrence or lack of distinct PAM motifs can distinguish between on-target and off-target edit sites.

CRISPR-Cas systems -> anti-CRISPR proteins

It includes those tools that facilitate the exploration of anti-CRISPR proteins. Anti-CRISPR proteins are a class of naturally occurring proteins that act as inhibitors of the CRISPR-Cas system. They function by binding to CRISPR-associated enzymes, such as Cas9, and preventing them from cleaving DNA.

Canonical gRNA design -> All tools

It includes the list of tools that assist in the design of gRNAs for canonical CRISPR-Cas experiments which mostly follows NHEJ or HDR pathways, emloying alignment-based & hypothesis-based, and learning-based approaches. The tools mostly consider gRNAs for experiments such as CRISPR knock-out, knock-in and gene regulation, excluding base editing and prime editing events.

Canonical gRNA design -> Alignment- & Hypothesis-based

It includes the list of tools that assist in the design of gRNAs for canonical CRISPR-Cas experiments which mostly follows NHEJ or HDR pathways, emloying alignment-based & hypothesis-based approaches. The tools mostly consider gRNAs for experiments such as CRISPR knock-out, knock-in and gene regulation, excluding base editing and prime editing events.

Canonical gRNA design -> Learning-based

It includes the list of tools that assist in the design of gRNAs for canonical CRISPR-Cas experiments which mostly follows NHEJ or HDR pathways, emloying learning-based approaches, which are based on machine learning algorithms after the study of large datasets.

Cas9 mutation prediction

It includes the list of tools for the prediction of outcomes from knock-out experiments resulting from double stranded breaks induced by CRISPR-Cas9.

Base editing -> All tools

The list comprises various tools which enable base editing for CRISPR-Cas experiments. It includes tools that assist in gRNA designs for various types of base editors and the prediction of editing efficiency and outcome patterns of such base editors.

Base editing -> Design

It includes tools that assist in gRNA designs for various types of base editors.

Base editing -> Outcome prediction

It includes tools that assist in the prediction of editing efficiency and outcome patterns of base editors.

Prime editing -> All tools

It includes the list of tools that aid in the design of pegRNAs for prime editing. The design of pegRNAs is more complicated than that of normal gRNAs due to the inherent complexity of their structure. It also consists of an efficiency prediction tool for pegRNAs.

Prime editing -> Design

It includes the list of tools that aid in the efficiency prediction tool for pegRNAs.

Prime editing -> Outcome prediction

It includes the list of tools that aid in the design of pegRNAs for prime editing.

Plant experiments

Within the list, sgRNA design tools that are specifically optimized for plant genomes are included. Most tools provide highly specific Cas9 targets and offer off-target prediction. It also consists of tools that aid in assembling CRISPR-Cas single guide and multiplex guide RNA constructs either for gene editing or gene regulation.

Analysis and visualization -> All tools

The list encompasses a range of tools for the downstream analysis of CRISPR-Cas experiments, that include canonical experiments (other than base editing and prime editing), base editing, prime editing, multipurpose tools and the ones used for CRISPR screens. These simple and quick tools accurately characterize and quantify the induced CRISPR edits more easily.

Analysis and visualization -> Multipurpose

It includes the list of tools that support more than one category of CRISPR-Cas editing technologies such as canonical Cas9 knock-out and knock-in, base editing and prime editing under a single platform.

Analysis and visualization -> Canonical experiments

The list comprises tools that support canonical CRISPR-Cas editing experiments resulting in NHEJ and HDR events, other than base editing and prime editing. Tools may use NGS data or Sanger sequencing data for analysis, whichever is compatible with the tool.

Analysis and visualization -> CRISPR screens

Within this list, those tools that provide functionality for the identification and selection of edited candidate hits from pooled screening data are included. These tools simplify the analysis and visualization of large datasets.

Analysis and visualization -> Base editing

It includes the list of tools that aid in the downstream analysis and visualization of base editing experiments. Tools may take NGS datasets or Sanger sequencing datasets as input.

Analysis and visualization -> Prime editing

This list comprises the tools that allow for the final assessment and visualization of insertions, deletions, and base conversions from the results of pegRNA mediated prime editing experiments.

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