Bioinformatics: GFF Phase Token Check Tool

Description

Parse one GFF phase token.

Genome annotations depend on coordinate origin, endpoint inclusion, strand and reading-phase conventions. A local offset or phase token can be handled precisely while a complete transcript, reference identity and biological reading frame remain separate validation questions.

Parse one GFF phase token.

When to use this tool

Use Bioinformatics: GFF Phase Token Check when checking the stated genomic coordinate, annotation phase or attribute-value convention.

How to use the tool and how it works

Enter token. Use the units and conventions below.
Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
Read result. Expand result to inspect the returned fields.

Parse one GFF phase token. Accept only zero, one, two or dot; known excludes dot, phase is its number or -1 for unknown.^[1]

Annotation frame/phase fields describe codon offsets under a strand-aware feature convention. A local token or carry calculation does not validate a transcript or translate its sequence.^[2]

Input field	Meaning and units	Accepted input
token	Token	Required. Text; one of "0", "1", "2", ".". Implementation limit: 8192 Unicode code points and 16384 UTF-16 code units.

Output field	Interpretation	Returned shape
result	Returned calculated value or nested object under the stated output convention.	Required. Object.
result.known	Supplied knowledge or lexical-recognition flag under the stated convention, without independent authentication.	Calculated result member: boolean.
result.phase	Numeric phase 0..2, or -1 sentinel when known=false.	Calculated result member: number.

json

{
  "input": {
    "token": "."
  },
  "output": {
    "result": {
      "known": false,
      "phase": -1
    }
  }
}

Limitations and assumptions

Unknown phase uses a sentinel; full annotation syntax, CDS ordering and reading-frame validity are not checked.
Outputs are nested inside result. Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.

Alternative or Complementary methods

Use the intended complete BED/GFF/GTF format, reference assembly and transcript model to validate full annotations and biological meaning.

References

Calculation and input contract: bioinformatics/gff-phase-token-check — tool.io
GFF/GTF file format — Ensembl

Similar or alternative tools

GFF3 Phase Strand Carry
Return CDS phase carry and strand-end convention.
CDS Frame Offset
Compute zero-based codon offset from an explicit spliced-CDS base count, distinct from a GFF phase field.