Sliding GC Content

Calculate GC content in complete DNA windows at a chosen step size.

Description

GC content can vary along a DNA sequence.

GC content can vary along a DNA sequence. Sliding windows summarize this variation at a specified resolution.

Calculate GC content in complete DNA windows at a chosen step size.

When to use Sliding GC Content

Use this for the following task: Calculate GC content in complete DNA windows at a chosen step size.

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

How to use Sliding GC Content 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, windowLength, stepLength using the field table, then run the tool.
Read windowStarts, gcPercent. 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
windowLength	Window length	integer; minimum 1	Required
stepLength	Step length	integer; minimum 1	Required

Normalize canonical DNA, require positive integer window/step lengths and a window that fits. Build cumulative GC counts and evaluate complete windows from zero in step increments.^[1]

GC% = 100 × (G+C count in window)/windowLength

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

Output field	Meaning	Value type
windowStarts	Zero-based start offsets of complete windows in the trimmed sequence.	list of integer
gcPercent	GC percent	list of number

json

{
  "input": {
    "sequence": "GGCCAAAA",
    "windowLength": 4,
    "stepLength": 4
  },
  "output": {
    "windowStarts": [
      0,
      4
    ],
    "gcPercent": [
      100,
      0
    ]
  }
}

Limitations and assumptions

Only full windows are included; starts are zero based. Window count is bounded, and no ambiguous-base handling or bias correction is added.

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 GC Skew for this operation: Calculate GC skew and compositional bias without inferring replication strand from skew alone. For a complementary task, use GC Coverage Dropout for this operation: Find GC bins with coverage deficits relative to a caller-supplied expected depth.

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

References

Sliding GC Content — tool.io

Similar or alternative tools

GC Skew
Calculate GC skew and compositional bias without inferring replication strand from skew alone.
GC Coverage Dropout
Find GC bins with coverage deficits relative to a caller-supplied expected depth.