Trusted by Leading Research & Pharma Institutions

sgRNA Design Service

Q: How do you calculate on-target efficiency scores?

We use the Doench Rule Set algorithm, which was developed by analyzing thousands of sgRNA experiments. The algorithm considers position-specific nucleotide preferences, GC content, and other sequence features to predict cleavage efficiency. Our platform uses the updated 2016 version which provides improved accuracy over earlier models.

Q: What off-target analysis do you provide?

Our platform performs genome-wide off-target analysis using the CFD (cutting Frequency Determination) scoring method. We identify all potential off-target sites with up to 4 mismatches and calculate positional mismatch penalties. Each sgRNA receives a comprehensive specificity score that considers all potential off-target sites in the genome.

Q: Which CRISPR systems do you support?

We support SpCas9, Cas12a (Cpf1), and prime editing systems. For SpCas9, we optimize for standard NGG PAM sequences. For Cas12a, we support TTTV PAM designs. For prime editing, we provide pegRNA design with nicking sgRNA recommendations and template optimization.

Q: How many sgRNAs should I order per gene?

We recommend ordering 3-5 sgRNAs per target gene for knockout experiments. Having multiple guides increases the probability of finding highly efficient editors. For knock-in experiments using HDR, we typically recommend 2-3 high-scoring guides combined with optimized donor templates.

Q: Can you design sgRNA libraries for screening?

Yes, we offer comprehensive sgRNA library design services. We can design genome-wide libraries, focused sub-libraries targeting specific gene pathways, and CRISPRi/CRISPRa libraries. All libraries include complete coverage analysis, negative controls, and ranking scores for each guide.

Q: What species do you support?

Our standard platform supports human, mouse, rat, zebrafish, and C. elegans. For other species, we can develop custom parameters based on genomic sequence analysis. Contact our team for species-specific requirements.

Accelerate your CRISPR experiments with our AI-powered sgRNA design platform. Maximize on-target activity while minimizing off-target effects using validated algorithms backed by peer-reviewed research.

AI-Powered Design

97% Efficiency

Off-Target Analysis

Learn More

Trusted by leading research and pharmaceutical institutions

MIT

Pfizer

Stanford

Roche

Johns Hopkins

Novartis

Why Choose Us

Doench Rule Set scoring algorithm

Comprehensive off-target analysis

Multi-species support

Expert consultation included

AI-Powered Design

Machine learning optimized sgRNA selection

Off-Target Analysis

Genome-wide specificity assessment

Multi-Cas Support

Cas9, Cas12a, and prime editing

Editing Efficiency

97%

Service Overview

Precision sgRNA Design for Every CRISPR Experiment

Our platform combines validated algorithms with comprehensive genome analysis to deliver optimal sgRNA recommendations for your specific experimental needs.

AI-Powered Algorithm

Our design platform leverages machine learning models trained on millions of sgRNA experiments to predict on-target efficiency and off-target potential with industry-leading accuracy.

Doench Rule Set scoring (updated 2016)
CFD off-target scoring
Multi-species optimization

Comprehensive Analysis

Every sgRNA recommendation includes detailed off-target analysis across the entire genome, ensuring you can make informed decisions for your experiments.

Genome-wide specificity check
Seed region analysis
GC content optimization

Instant Results

Get sgRNA recommendations within seconds for any gene in supported species.

Flexible Options

Support for Cas9, Cas12a, and prime editing systems with customizable parameters.

Expert Support

Ph.D.-level scientists available for consultation on complex design projects.

Technology Platform

Validated Algorithms for sgRNA Design

Our platform is built on peer-reviewed algorithms and continuously validated against experimental data.

On-Target Scoring

Doench Rule Set algorithm predicts sgRNA efficiency based on sequence features and position-specific nucleotides.

Doench 2016 Validated

Off-Target Analysis

CFD scoring evaluates potential off-target sites across the genome with mismatch position weighting.

CFD Score Genome-wide

Multi-Cas Support

Optimized parameters for SpCas9, Cas12a, and emerging CRISPR systems including prime editing.

Cas9 Cas12a Prime

Design Principles

GC Optimal GC content: 40-70%

Seed Seed region high specificity

PAM PAM sequence optimization

Exon Early exon targeting preferred

Sequences to Avoid

Poly-T Poly-T (>4 consecutive T)

Homopol Long homopolymers avoided

Low GC Very low GC (<30%)

High Hom High homology to off-targets

Specifications

Flexible Options for Diverse Needs

Comprehensive specifications to meet your research requirements.

Parameter	Standard Design	Premium Design	Custom Project
Species Support	Human, Mouse, Rat	All major model organisms	Any species on request
Cas Proteins	SpCas9	Cas9, Cas12a	Custom Cas variants
sgRNAs per Gene	3-5 recommended	Up to 10 ranked options	Unlimited analysis
On-Target Scoring	Doench Rule Set	Doench + custom models	Bespoke algorithms
Off-Target Analysis	Genome-wide scan	CFD + positional analysis	Comprehensive report
Delivery Format	Online report + CSV	Detailed PDF + sequence files	Custom formats

Workflow

Streamlined Process from Design to Delivery

Our proven workflow ensures optimal sgRNA selection at every stage.

Input

Submit gene name or sequence

Analyze

AI-powered sgRNA scanning

Validate

Off-target verification

Rank

Score-based prioritization

Deliver

Comprehensive report

Applications

Diverse Applications Across Biotechnology

Our sgRNA design services support research and development in multiple fields.

Precision Gene Editing

Optimized sgRNA design for knockout, knock-in, and base editing applications. Our algorithms maximize editing efficiency while minimizing unwanted modifications.

Single gene knockout
HDR-mediated knock-in
Base editing optimization
Prime editing pegRNA design

97%

Average editing efficiency

High-Throughput Screening

Comprehensive sgRNA library design for genome-wide and focused screening applications. Consistent coverage and scoring across all guides ensure robust screening results.

Genome-wide libraries
Focused sub-library design
CRISPRi/CRISPRa libraries
Pooled screening optimization

50K+

sgRNAs designed monthly

Therapeutic Development

High-fidelity sgRNA design for gene therapy applications. Stringent off-target analysis and GMP-compatible design workflows support clinical development.

Ex vivo cell therapy
In vivo gene editing
cGMP design documentation
Regulatory support

IND

Clinical trial support

Testimonials

What Our Clients Say

Trusted by researchers worldwide for quality and reliability.

"The sgRNA recommendations were spot-on. Every guide we ordered from their top picks showed excellent editing efficiency in our experiments. Highly recommended!"

Senior Scientist

Biotechnology Company

"We redesigned our entire screening library using their platform. The improvement in our hit rates was remarkable. Their off-target analysis saved us weeks of validation work."

Research Director

Academic Research Institution

"The platform's integration with our workflow was seamless. Their Ph.D. support team helped optimize our prime editing strategy significantly."

Lead Researcher

Pharmaceutical Company

Scientific Literature

Scientific Foundation

Our platform is backed by peer-reviewed research.

523 Citations

Design and analysis of CRISPR-Cas experiments

Hanna RE, Doench JG. Nature Biotechnology. 2020.

Comprehensive review of CRISPR-Cas experiment design tools and analytical methods for large-scale screening data.

View DOI

312 Citations

CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off-Target Evaluation

Manghwar H, Li B, Ding X, et al. Advanced Science. 2020.

Extensive review covering sgRNA design rules, off-target assessment methods, and strategies to minimize off-target effects.

View DOI

86 Citations

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency

Hiranniramol K, Chen Y, Liu W, Wang X. Bioinformatics. 2020.

Development of sgDesigner using stacked generalization framework for improved sgRNA activity prediction.

View DOI

78 Citations

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

Henkel L, Rauscher B, Schmitt B, Winter J, Boutros M. BMC Biology. 2020.

Empirical design criteria for optimized sgRNA libraries in genome-wide CRISPR screening applications.

View DOI

64 Citations

C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

Liu G, Zhang Y, et al. Methods. 2020.

Hybrid CNN-GRU architecture for improved sgRNA cleavage efficiency prediction across multiple datasets.

View DOI

FAQ

Frequently Asked Questions

Find answers to common questions about our service.

We use the Doench Rule Set algorithm, which was developed by analyzing thousands of sgRNA experiments. The algorithm considers position-specific nucleotide preferences, GC content, and other sequence features to predict cleavage efficiency. Our platform uses the updated 2016 version which provides improved accuracy over earlier models.

Our platform performs genome-wide off-target analysis using the CFD (cutting Frequency Determination) scoring method. We identify all potential off-target sites with up to 4 mismatches and calculate positional mismatch penalties. Each sgRNA receives a comprehensive specificity score that considers all potential off-target sites in the genome.

We support SpCas9, Cas12a (Cpf1), and prime editing systems. For SpCas9, we optimize for standard NGG PAM sequences. For Cas12a, we support TTTV PAM designs. For prime editing, we provide pegRNA design with nicking sgRNA recommendations and template optimization.

We recommend ordering 3-5 sgRNAs per target gene for knockout experiments. Having multiple guides increases the probability of finding highly efficient editors. For knock-in experiments using HDR, we typically recommend 2-3 high-scoring guides combined with optimized donor templates.

Yes, we offer comprehensive sgRNA library design services. We can design genome-wide libraries, focused sub-libraries targeting specific gene pathways, and CRISPRi/CRISPRa libraries. All libraries include complete coverage analysis, negative controls, and ranking scores for each guide.

Our standard platform supports human, mouse, rat, zebrafish, and C. elegans. For other species, we can develop custom parameters based on genomic sequence analysis. Contact our team for species-specific requirements.

sgRNA Design Service

Why Choose Us

AI-Powered Design

Off-Target Analysis

Multi-Cas Support

Precision sgRNA Design for Every CRISPR Experiment

AI-Powered Algorithm

Comprehensive Analysis

Instant Results

Flexible Options

Expert Support

Ready to Optimize Your CRISPR Experiments?

Validated Algorithms for sgRNA Design

On-Target Scoring

Off-Target Analysis

Multi-Cas Support

Design Principles

Sequences to Avoid

Flexible Options for Diverse Needs

Streamlined Process from Design to Delivery

Input

Analyze

Validate

Rank

Deliver

Diverse Applications Across Biotechnology

Precision Gene Editing

High-Throughput Screening

Therapeutic Development

What Our Clients Say

Scientific Foundation

Design and analysis of CRISPR-Cas experiments

CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off-Target Evaluation

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

Frequently Asked Questions

Ready to Start Your Project?

Recommended Services

Related Resources

Request a Quote

sgRNA Design Service

Why Choose Us

AI-Powered Design

Off-Target Analysis

Multi-Cas Support

Precision sgRNA Design for Every CRISPR Experiment

AI-Powered Algorithm

Comprehensive Analysis

Instant Results

Flexible Options

Expert Support

Ready to Optimize Your CRISPR Experiments?

Validated Algorithms for sgRNA Design

On-Target Scoring

Off-Target Analysis

Multi-Cas Support

Design Principles

Sequences to Avoid

Flexible Options for Diverse Needs

Streamlined Process from Design to Delivery

Input

Analyze

Validate

Rank

Deliver

Diverse Applications Across Biotechnology

Precision Gene Editing

High-Throughput Screening

Therapeutic Development

What Our Clients Say

Scientific Foundation

Design and analysis of CRISPR-Cas experiments

CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off-Target Evaluation

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

Frequently Asked Questions

Ready to Start Your Project?

Recommended Services

Related Resources