General feature format

In bioinformatics, the general feature format is a file format used for describing genes and other features of DNA, RNA and protein sequences.

GFF Versions

The following versions of GFF exist:

, generally deprecated
*, a derivative used by Ensembl

*, with additional pragmas and attributes for sequence_alteration features

GFF2/GTF had a number of deficiencies, notably that it can only represent two-level feature hierarchies and thus cannot handle the three-level hierarchy of gene → transcript → exon. GFF3 addresses this and other deficiencies. For example, it supports arbitrarily many hierarchical levels, and gives specific meanings to certain tags in the attributes field.
The GTF is identical to GFF, version 2.

GFF general structure

All GFF formats are tab delimited with 9 fields per line. They all share the same structure for the first 7 fields, while differing in the content and format of the ninth field. Some field names have been changed in GFF3 to avoid confusion. For example, the "seqid" field was formerly referred to as "sequence", which may be confused with a nucleotide or amino acid chain. The general structure is as follows:

Position index	Position name	Description
1	seqid	The name of the sequence where the feature is located.
2	source	The algorithm or procedure that generated the feature. This is typically the name of a software or database.
3	type	The feature type name, like "gene" or "exon". In a well structured GFF file, all the children features always follow their parents in a single block. In GFF3, all features and their relationships should be compatible with the .
4	start	Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED.
5	end	Genomic end of the feature, with a 1-base offset. This is the same end coordinate as it is in 0-offset half-open sequence formats, like BED.
6	score	Numeric value that generally indicates the confidence of the source in the annotated feature. A value of "." is used to define a null value.
7	strand	Single character that indicates the strand of the feature. This can be "+", "-",, ".", or "?" for features with relevant but unknown strands.
8	phase	phase of CDS features; it can be either one of 0, 1, 2 or ".". See the section below for a detailed explanation.
9	attributes	A list of tag-value pairs separated by a semicolon with additional information about the feature.

The 8th field: phase of CDS features

Simply put, CDS means "Coding DNA Sequence". The exact meaning of the term is defined by Sequence Ontology. According to the GFF3 specification:

Meta Directives

In GFF files, additional meta information can be included and follows after the ## directive. This meta information can detail GFF version, sequence region, or species.

GFF software

Servers

Servers that generate this format:

Clients

Clients that use this format:

Name	Description	Links
GBrowse	GMOD genome viewer
IGB	Integrated Genome Browser	Integrated Genome Browser
Jalview	A multiple sequence alignment editor & viewer	Jalview
STRAP	Underlining sequence features in multiple alignments. Example output:
JBrowse	JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5
ZENBU	A collaborative, omics data integration and interactive visualization system

Validation

The modENCODE project hosts an with generous limits of 286.10 MB and 15 million lines.
The Genome Tools software collection contains a gff3validator tool that can be used offline to validate and possibly tidy GFF3 files. An is also available.