Analysis

CpG island finder

Find CpG islands by either published definition: Gardiner-Garden & Frommer 1987 (GC > 50%, observed/expected CpG > 0.6, >= 200 bp — the original, which also calls many Alu repeats) or Takai & Jones 2002 (GC >= 55%, obs/exp >= 0.65, >= 500 bp — written to exclude them). Windows are merged only where the merged region STILL meets the criteria, so every island returned satisfies the definition it is reported under. Reports the CpG DINUCLEOTIDE count separately from GC content, because conflating the two is the usual way this number goes wrong.

post/cpg_islands

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/cpg_islands
  • Auth: none required

Request body

sequencestring required

DNA to scan (raw or FASTA). Max 5,000,000 bases.

preset'gardiner-garden' | 'takai-jones'

Which published criteria to apply. "gardiner-garden": Gardiner-Garden & Frommer 1987 (GC > 50%, obs/exp > 0.6, >= 200 bp; thresholds strict, as the paper states them) "takai-jones": Takai & Jones 2002 (GC >= 55%, obs/exp >= 0.65, >= 500 bp; excludes most Alu)

minGcPctnumber

Override the preset's GC threshold, 0-100.

minObsExpnumber

Override the preset's observed/expected CpG threshold.

minLengthinteger

Override the preset's minimum island length, bp.

windowSizeinteger

Scanning window in bp. 200 is Takai & Jones' window, and it is used for both presets so the two differ only in their thresholds (Gardiner-Garden & Frommer's 1987 paper scanned 100 bp windows).

mergeGapinteger

Join passing regions closer than this, when the joined region still passes. Takai & Jones use 100.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.