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GC Content Profile (Sliding Window)

Plot the GC content along a DNA sequence in a sliding window of a size and step you choose, and find the most GC-rich and GC-poor stretches.

Formula

GCwindow %=G+CA+C+G+T×100(counts in the window)\mathrm{GC}_{\text{window}}\,\% = \dfrac{G + C}{A + C + G + T}\times 100\quad(\text{counts in the window})
windows start at 1, 1+s, 1+2s, … (s=step)\text{windows start at } 1,\ 1 + s,\ 1 + 2s,\ \ldots\ (s = \text{step})
window\text{window}
number of consecutive bases counted at each point
step\text{step}
how far the window moves between points

How it works

GC content is rarely uniform along a sequence. Coding regions, promoters, CpG islands, replication origins and horizontally acquired genes can differ from their surroundings. Sliding a window along the sequence and plotting its GC content shows those differences.

A smaller window shows finer detail but is noisier, because each point rests on fewer bases; a larger window is smoother but blurs short features. The dashed line marks the average over the whole sequence.

Worked example

A 108-base illustrative sequence alternating AT-rich and GC-rich stretches, window 20, step 5.

  1. The first window covers bases 1 to 20, the second 6 to 25, and so on.
  2. There are (108 − 20) / 5 + 1 = 18 windows.

Overall GC of 50.9%, with the most GC-rich window at 75.0% (bases 36 to 55) and the poorest at 25.0% (bases 51 to 70).

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • Windows contain only unambiguous bases. A window with no A, C, G or T is skipped.
  • The position plotted is the centre of the window.
  • At most 2,000 windows are drawn.

Common mistakes

  • Interpreting a peak from a very small window as a real feature. Check it with a larger window.
  • Comparing profiles made with different window sizes.
  • Treating a dip in GC as evidence of a gene boundary. It is a hint to investigate, not a conclusion.

Related tools

GC Content CalculatorGC percentage and base composition of a sequenceOpen calculatorFASTA Sequence AnalyzerLength, GC, base counts and CpG ratio for one or many sequencesOpen calculatorORF FinderOpen reading frames in all six frames, ATG to stopOpen calculatorPrimer Tm Calculator (Four Methods)Primer melting temperature by four accepted methods, side by sideOpen calculator