GC Skew

Calculate GC skew and compositional bias without inferring replication strand from skew alone.

Description

GC skew compares guanine and cytosine abundance.

GC skew compares guanine and cytosine abundance. Its sign describes sequence composition, without uniquely determining replication-strand identity.

Calculate GC skew and compositional bias without inferring replication strand from skew alone.

When to use GC Skew

Use this for the following task: Calculate GC skew and compositional bias without inferring replication strand from skew alone.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use GC Skew and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter sequence, neutralTolerance using the field table, then run the tool.
Read gCount, cCount, gcSkew, bias. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
sequence	Sequence	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required
neutralTolerance	Absolute skew at or below this fraction is near-balanced.	number; minimum 0; maximum 1	Required

Normalize canonical DNA, require at least one G or C, and compare skew with ±tolerance. Equality belongs to near-balanced.^[1]

skew = (G−C)/(G+C)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
gCount	G count	integer
cCount	C count	integer
gcSkew	GC skew	number
bias	Bias	string

json

{
  "input": {
    "sequence": "GGGC",
    "neutralTolerance": 0.1
  },
  "output": {
    "gCount": 3,
    "cCount": 1,
    "gcSkew": 0.5,
    "bias": "G-enriched"
  }
}

Limitations and assumptions

Sequences lacking G/C produce an input error rather than an arbitrary zero. Replication origins are not inferred.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose AT Skew for this operation: Calculate AT skew as (A−T)/(A+T) from a canonical DNA sequence. For a complementary task, use Sliding GC Content for this operation: Calculate GC content in complete DNA windows at a chosen step size.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

GC Skew — tool.io

Similar or alternative tools

AT Skew
Calculate AT skew as (A−T)/(A+T) from a canonical DNA sequence.
Sliding GC Content
Calculate GC content in complete DNA windows at a chosen step size.