CpG Parameter Calculator

The following values will be calculated for a given sequence:

Length of sequence
Total CpG dinucleotide count
Total stimulatory CpG motif count
Total inhibitory CpG motif count
% CpG: Percent of sequence that is composed of CpGs
RF3: Metric that differentially weights and sums both stimulatory and inhibitory motifs (see more information) to create a global estimate of the TLR9 stimulatory (+) or inhibitory (-) potential of a given sequence.
nRF3 (RF3 normalized to the human genome)

Step 1 (optional)

Step 2

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CpG Depletion Tool

Use this tool to removed CpG dinucleotides from a sequence.

Is this a coding region?

Yes

What is the host species in which the AAV will be administered?

Mouse (Mus musculus)

Rat (Rattus norvegicus)

Human (Homo sapiens)

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Welcome to CpG Assist Tool (CpGAT)

This tool has three primary functions:

CpG Parameter Calculator

Quantify CpG content for a single-stranded DNA sequence you provide (copy-paste or upload in FASTA format).

AAV Component Explorer

Visualize and explore CpG content of a library of commonly used AAV transgenes, promoters, ITRs, and miscellaneous components.

CpG Depletion Tool

Depletes CpG dinucleotides from a sequence you provide. For coding sequences, host-specific, codon-optimized synonymous mutations are made. Current host options: Mouse, Rat, & Human. For noncoding sequences, GC content is kept as consistent as possible while removing CG dinucleotides.

This tool is described in an accompanying paper:

paper citation here

CpGAT is based, in part, on work by J. Fraser Wright:

Wright, J. F. (2020). Quantification of CpG Motifs in rAAV Genomes: Avoiding the Toll. Molecular Therapy, 28(8), 1756–1758.

Disclaimer: The goal of this application is to provide the tools we have developed to the broader research community. This application is for research guidance only and should be used with discretion.

CpGAT was created and is maintained by C. Dunn and L. Boulanger, Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University.

Created by: Connor Dunn

The basis for this tool is described in an accompanying paper

RF3 was created by J. Fraser Wright and presented in this paper.

Contact Information:

Connor Dunn¹ -> cedunn@princeton.edu

Lisa Boulanger^1,² (Principal Investigator) -> lboulang@princeton.edu

¹Princeton University Department of Molecular Biology ²Princeton Neuroscience Institute

This application was built using Shiny for Python, which is supported by Posit. Click here to learn more about Shiny for Python.

CpG Parameter Calculator

The following values will be calculated for a given sequence:

AAV Component Explorer

Use this explorer to visualize the CpG Parameters of various commonly used AAV components.

CpG Depletion Tool

Use this tool to removed CpG dinucleotides from a sequence.

Welcome to CpG Assist Tool (CpGAT)

This tool has three primary functions:

CpG Parameter Calculator

Quantify CpG content for a single-stranded DNA sequence you provide (copy-paste or upload in FASTA format).

AAV Component Explorer

Visualize and explore CpG content of a library of commonly used AAV transgenes, promoters, ITRs, and miscellaneous components.

CpG Depletion Tool

Depletes CpG dinucleotides from a sequence you provide. For coding sequences, host-specific, codon-optimized synonymous mutations are made. Current host options: Mouse, Rat, & Human. For noncoding sequences, GC content is kept as consistent as possible while removing CG dinucleotides.

This tool is described in an accompanying paper:

CpGAT is based, in part, on work by J. Fraser Wright:

Disclaimer: The goal of this application is to provide the tools we have developed to the broader research community. This application is for research guidance only and should be used with discretion.

CpGAT was created and is maintained by C. Dunn and L. Boulanger, Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University.