What this GFF3 inspector checks
Every feature must have nine tab-separated columns with positive 1-based inclusive coordinates, a valid score marker, strand, and phase. Column 9 is parsed as case-sensitive tag/value attributes with GFF3 percent decoding. Sequence-region directives provide explicit bounds, while an optional embedded FASTA provides independent sequence-length bounds.
ID, Parent, and CDS checks
Repeated IDs are allowed for discontinuous features when their identifying columns remain consistent. Parent values are resolved against those ID groups, then checked for self-links, cycles, later definitions, and coordinate containment. CDS segments grouped by parent and strand are ordered biologically and checked for phase progression. These structural checks cannot decide whether the biological model itself is correct.
Validation boundary
This is a bounded structural preflight, not complete GFF3 or submission validation. It does not load Sequence Ontology releases, enforce ontology-specific parent/type relationships, apply NCBI or Ensembl submission profiles, validate Target/Gap semantics, translate CDS sequences, verify splice sites, compare an external reference FASTA, or repair annotations. A clean result only means the supported checks found no errors.
Frequently asked questions
Why can the same ID occur on multiple rows?
GFF3 allows a discontinuous feature to span multiple locations. Its rows may share an ID, but they must collectively describe one feature; inconsistent seqid, source, type, or strand is reported.
Is GFF3 the same as GTF?
No. They share nine columns, but column 9 and relationship conventions differ. This parser expects GFF3 tag=value attributes, not GTF’s quoted attribute syntax.
Does a phase warning prove the CDS is wrong?
No. It identifies a mathematical discontinuity in ordered segments for one parent. Alternative conventions or unusual models still require expert review.
Authoritative reference
The Sequence Ontology GFF3 specification defines the columns, directives, escaping, reserved attributes, hierarchy rules, and embedded FASTA section used by this audit.
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