Methylation Context

Classify a cytosine as CG, CHG, or CHH context.

Description

Methylation context distinguishes CpG and non-CpG sequence environments.

Methylation context distinguishes CpG and non-CpG sequence environments.^[1]

Classify a cytosine as CG, CHG, or CHH context.

When to use Methylation Context

Use this tool to classify a cytosine as CG, CHG, or CHH context.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use Methylation Context and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter sequenceContext using the field table and calculation rules, then run the tool.
Read contextClass, valid. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequenceContext	Sequence context	string	Required

Trim/uppercase and inspect the first three characters. Return context and validity; unknown context returns invalid successfully.

CG prefix→CG; C[ACT]G→CHG; C[ACT][ACT]→CHH

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
contextClass	Context class	string; one of "CG", "CHG", "CHH", "invalid"
valid	Valid context	boolean

json

{
  "input": {
    "sequenceContext": "CAG"
  },
  "output": {
    "contextClass": "CHG",
    "valid": true
  }
}

Limitations and assumptions

A CG prefix passes without third-character validation. No complete sequence, strand or genomic locus is validated.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Bisulfite Primer CpG Check: Count CpGs in bisulfite primer sequences against a supplied maximum. For a complementary task, use CPG Region Classifier: Classify a CpG’s distance from a caller-supplied island.

References

Methylation Context — tool.io

Similar or alternative tools

Bisulfite Primer CpG Check
Count CpGs in bisulfite primer sequences against a supplied maximum.
CPG Region Classifier
Classify a CpG’s distance from a caller-supplied island.