Home » News » CRISPR Design Tools for Genome Editing: the full list with description

crispr tools targetIn just four years, CRISPR has revolutionized approaches to genome editing. Inexpensive to build and easy to use, CRISPR (Clustered, Regularly Interspaced. Short Palindromic Repeats) has gained worldwide attention for its ability to target specific locations in the genetic code of any organism with just two elements – guide RNA and an enzyme called Cas9.

CRISPR was originally discovered as a genetic phenomenon in archaea and certain bacteria – an immune response that could be adapted for purposes of modifying the genes of higher organisms. Applications of crispr system design include genetic moderation of crops, gene therapies for diseases such as cancer, and synthesizing drug-producing microbes. CRISPR’s applications may be even more far-reaching in the future – but some fine-tuning is required to reach its full potential.

Though CRISPR allows quick, inexpensive genetic editing in virtually any lab, its accuracy can be impaired by the guide RNA’s activity in other locations on the genome. In an effort to improve CRISPR’s precision and eliminate these “off target” results, a number of crispr design tools have been developed interdentally by universities and biotech companies around the world.

These crispr tools are typically web or cloud based, and many are free and open source, making it possible for anyone to obtain guide RNA sequences, select parameters and search the genome for off targets. With these CRISPR tools, gene editing and modification becomes streamlined and efficient, without the need for customizing the editing tool for each use. Let’s see all of the most useful CRISPR design tools.

crispr tool action

Benchling CRISPR gRNA Design

Active, targeted gNRA is essential to guide the CAS9 nuclease to a specific location in the desired genome. The Benchling CRISPR gRNA Design system allows users to design optimal gRNAs for better targeting. This web-based crispr design tool allows users to quickly analyze the target location and isolate the desired sequences. This tool searches the entire genome for targets and returns all results. The Benchling CRISPR gRNA Desugn tool supports up to four mismatches, and users can customize the PAM (photospacer adjacent motif) sequences.


Developed by Seoul National University, the Cas-OFFinder is an algorithm that quickly searches for possible off-target sites of Cas9 nucleases guided by gRNA. This crisper recognition tool d searches the entire genome for off-targeting and supports up to 10 mismatches. The Ca-OFFinder is a crispr recognition tool that supports 4 PAM sequences, but does not predict gRNA activity.


From the University of Heidelberg, CCTop is an online predictor for CRISPR/Cas9 that supports 11 PAM types and up to 5 gRNA mismatches in a search of the whole genome. This crispr tool searches the entire genome and returns all off target results, but does not predict gRNA activity.

crispr tool CTop


Harvard University’s CHOPCHOP is a web-based crispr tool designed to support precise cuts in the genome. This free online editing tool allows users to target a specific region of the gene and to fine tune targeting options with toggle features. CHOPCHOP supports up to two mismatches and allows 4 PAM sequences in its simple user interface.

crispr tool CHOPCHOP


COD, or Cas9 Online Designer, was developed by China’s Syncotech in collaboration with Nanking University and China Medical University. This crispr design tool screens Cas9 targets as well as off-targets. It offers high-throughput efficiency with an off target-scoring matrix. This tool offers a fast and flexible gene knockout pipeline and reports between 0 and 8 mismatches.

CRISPR Configurator & Specificity Tool

From Dharmacon, the CRISPR Configurator and Specificity Tool allows users to design custom guide RNAs with an online interface that also allows for entering designs created outside the program. With the Configurator’s tool set, users can select CRISPER targeting sequences for inserting into genes, or choose from redesigned synthetic RNA sequences. With 3 design options, the CRISPR Configurator & Specificity Tool supports up to 8 mismatches.


The Zhang Lab at MIT offers this simple online tool for entering sequence types, target genomes and sequencing. Upon submitting a query, users receive a custom gRNA design and analysis pf the specified parameters. This tool can search the entire genome for matches and can support 4 mismatches and two PAM sequences.

CRISPR gRNA Design Tool

From biotech lab DNA 2.0 comes this free online crispr design tool that allows users to either design a new gRNA or import one designed elsewhere. Users can select a species and PAM sequence as well as set off target parameters. This tool makes it possible to target either a specific gene or a genomic region, and results are downloadable or storable for future use. The CRISPR gRNA Design Tool can search the entire genome for targets, and returns all the genome’s targets.


Bioconductor, a free and open source design software project dedicated to the analysis of genomic data, produces CRISPRseek, a tool intended to find and filter potential guide RNAs. This design tool is capable of searching the entire genome for targets and returning all targets from the search. With any number of mismatches supported, this tool also offers user customizable PAM sequences.


Desktop Genetics has created DESKGEN, a crispr design tool that offers the functionality of a CRISPR tool with the accessibility of a genome browser. Its free editing interface allows users to access a wide range of supporting tools for storing, sharing and editing data. It offers fully customizable PAM sequences, searches the entire genome for targets, and supports an unlimited number of mismatches.crispr tool  - Deskgen


Thomas Jefferson University has created Off-Spotter, a crispr design tool that identifies all instances in the genome of a given gRNAs and PAM. Supporting a maximum of 5 mismatches, this tool allows users to select genome type, PAM and seed positions. This crispr tool is able to search an entire genome for targets and returns all targets of the genome.

sgRNA Designer

The Broad Institute of MIT and Harvard has produced the sgRNA Designer, a crispr tool designed to select and rank single guide RNA candidates for sequencing. The scope of the sgRNA Designer is limited to just one PAM sequence. Although this crispr tool can predict gRNA activity, it offers no support for mismatches and does not search the entire genome for targets.

CRISPR is not the first genome-dieting tool, but it is the newest, and it has the potential to change the field forever. CRISPR’s simple tools make sophisticated gene modification of any organism available to virtually any lab, cheaply and efficiently. Unlike other genome editors CRISPR does not have to be customized for each experiment – a key advantage to cutting costs and making the tools accessible worldwide.

Though CRISPR’s “scissor” tools – guide RNA and the Cas9 enzyme nuclease – are simple, they can target precise locations on a genome for cutting or modification. But for all CRISPR’s promised as a quick and versatile genome editor capable of precision targeting, it can make errors, mutating the wrong gene instead of the target. Searching for those “off targets” throughout the genome sequences could be time consuming and costly, and the potential for error remains high.

The long list of CRISPR tools has been developed by private companies and institutions around the world to hone CRISPR’s precision targeting. These software algorithms enable CRISPR users to search for off targets quickly and easily, and obtain corrected sequences of “good” guide RNAs.

Most of the new CRISPR system tools are web-based and free, with sophisticated options for fine tuning the gene selection process and setting parameters for precise gene modification. These tools require only a few clicks of the mouse to select desired genomes, enter sequences and more.

Because CRISPR is low cost and easily accessed and its suite of tools from sources ranging from leading research institutions such as Harvard and MIT to private biotech companies including Dharmacon and DNA 2.0. These tools put CRISPR’s power in the hands of researchers across the globe, and they open new doors for advances in genetic research that might have been unheard of a decade ago.

CRISPR is already in wide use for lab research on genomes ranging from human to zebrafish. Current applications of CRISPR technology include the development of gene therapies for the treatment of caner and other diseases, as well as microbes for the synthesis and production of new drugs. CRISPR design tools can also be used to modify crops to raise yield and nutritional content, and it can also be used to develop biological agents for tackling environmental disasters such as oil spills.

But CRISPR’s applications can go much farther. As the easy to use and readily available CRISPR technology puts sophisticated gene editing tools at the fingertips of nearly every researcher, it may be possible for anyone to reap the benefits of genetic tweaking – but these benefits are not without controversy.

CRISPR design opportunities

crispr tool oppotunitiesCRISPR tools could be used to eliminate a variety of inheritable conditions – or to enhance certain human or animal characteristics with an edit or action of imported DNA. CRISPR’s ability to edit the genome of just about any creature raises the specter of editing human genomes to create a new kind of human, one with abilities and lifespan far superior to existing people. Animals too could be modified to build in new traits and eliminate undesirable ones. Likewise, “supercrops” could become hardier and more productive, making food more accessible around the world.

That way CRISPR becomes more and more popular among investors who sees its potential and perspectives. There are not many ways to invest in CRISPR but several, such as Editas IPO or CRISPR domain names may be already easily found (you may see such an offer for example).

The simple toils of the latest and most sophisticated gene modification and editing system make innovation in genetic modification possible in labs large and small. With its long list of free, open source and cloud based editing tools and the ongoing development of new ones, CRISPR allows researchers to push the boundaries of a genetic modification on virtually any organism, with outcomes that are simultaneously promising and troubling. For users of CRISPR and its growing list of software tools, the future is now. But those applications of CRISPR system design technology are on the way to something new. And maybe soon people would calculate their own genome edits just as now we calculate a price when we buy a car?

Read the latest CRISPR-news on crisprsystem.com.

2 Replies to “CRISPR Design Tools for Genome Editing: the full list with description”

  1. Micah Reuss says:

    Wow, this was cool. Keep writing this kind of blogs, you will get a lot of people to this post if you continue working on this. I will be visiting this website more often. thx!

  2. Danny says:

    What are genome editing and CRISPR-Cas9 ? … and more efficient than other existing genome editing methods. CRISPR – Cas9 was adapted from a naturally occurring genome …

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