GFF3

GFF3, or General Feature Format Version 3, is a text-based file format used to describe genomic features and their coordinates on reference sequences. It is widely used in genome annotation pipelines because it provides a simple, machine-readable representation and supports hierarchical relationships among features such as genes, transcripts, and exons.

A GFF3 file is tab-delimited and comprises lines that describe individual features. Each data line contains nine columns: seqid, source, type, start, end, score, strand, phase, and attributes. Lines starting with a hash (#) are comments or directives; a line containing ##FASTA indicates that following lines contain sequence data in FASTA format. Coordinates are 1-based and inclusive; the type field generally uses terms from the Sequence Ontology.

The final column, attributes, is a semicolon-separated list of key=value pairs. Common keys include ID, Name, and Parent, with Parent used to express hierarchical relationships (for example a gene has an mRNA child, which in turn has exon children). The ID value must uniquely identify the feature, while the Name provides a human-readable label.

GFF3 is designed to be flexible and interoperable. The Type field relies on a controlled vocabulary, and the hierarchy created by Parent relationships enables complex models of gene structure. It is compatible with genome browsers and annotation pipelines, and is often contrasted with the GTF format.

Usage notes: many tools can parse GFF3, including libraries in Biopython, BioPerl, and others; ensure consistent sequence identifiers across files and include a proper FASTA section if provided. A simple GFF3 example would describe a gene feature with an ID, a transcript with a Parent pointing to the gene, and exons with Parent set to the transcript.