How to Find CpG Islands in Seqqio: GC Content, Observed/Expected CpG, and Window Settings

The tool is a transparent sequence-composition screen identified as Seqqio-CpGIslands-v1. It does not label promoters, methylation state, expression, or regulatory function. Keeping that boundary explicit is essential because “CpG island” has more than one operational definition.

Open CpG Islands and start with the defaults: a 200-base window, step 1, minimum island length 200 bases, minimum GC 50%, and minimum observed/expected CpG ratio 0.60. Seqqio uses strict comparisons, so a window must be greater than both percentage thresholds; equality alone does not qualify.

For a window of length W, Seqqio calculates GC% as 100 × (C + G) / W. Expected CpG is C × G / W; the observed count is the number of overlapping CG dinucleotides. The ratio is observed divided by expected. A GC-rich sequence can therefore fail the CpG-ratio test when C and G occur often but rarely next to each other.

Click Load example. Seqqio loads three synthetic records and restores the default criteria: a GC-rich central region with AT-rich flanks, a GC-rich but CpG-depleted control, and a low-GC control. Run the analysis in batch mode and compare the outcomes record by record. None of the controls is a genomic annotation.

The comparison tests the two-threshold logic. The enriched region can pass both local measures; the GC-rich depleted control demonstrates why GC content alone is insufficient; and the AT-rich control provides a low-composition baseline. If a record is shorter than the selected window, Seqqio reports it as not assessed rather than declaring that no island exists.

Qualifying windows that touch or overlap are consolidated into candidate islands. The displayed interval can therefore be longer than one window. Inspect its one-based coordinates and length, then read the recalculated GC percentage and CpG ratio for the complete merged region. Those final values describe the reported interval; they are not merely copied from its strongest window.

The classic criteria are not the only published choice. Takai and Jones compared the commonly used 200-base, 50% GC, 0.60 ratio definition with stricter 500-base, 55% GC, 0.65 criteria intended to reduce repetitive Alu-associated regions. Their study also makes clear that the definition is operational and purpose dependent.

EMBOSS likewise states in its cpgplot documentation that there is no single definition. Record your Seqqio parameters whenever results are compared across datasets or tools. Different windows, steps, threshold operators, and merging rules can produce different boundaries even when each implementation is internally correct.

A positive result supports a compositional statement about the supplied A/C/G/T sequence under the selected settings. It does not demonstrate an unmethylated state, a promoter, transcription, chromatin accessibility, or gene regulation. Ambiguous bases, RNA, gaps, or other symbols cause that record to fail rather than being silently removed.

Use the tool for transparent local sequence screening, parameter sensitivity checks, teaching observed/expected CpG, or creating traceable candidate intervals for follow-up. Use epigenomic assays and annotation resources when the question concerns methylation or biological regulatory activity.

CpG Islands is included in Seqqio's 39-application Windows 64-bit toolkit. The Seqqio overview describes the common FASTA, batch, history, and export workflow. Seqqio is offered as a US$99 one-time purchase with no activation key.

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