GFF and GTF formats

GFF files

Many bioinformatics programs represent genes and transcripts in GFF format (General Feature Format) which simply describes the locations and the attributes of gene and transcript features on the genome (chromosome or scaffolds/contigs).
GFF has many versions, but the two most popular that are GTF2 (Gene Transfer Format, described here) and GFF3 (defined here). Here are a few details about how these formats are commonly interpreted by bioinformatics programs.

GTF files

As seen in the GTF2 specification, the transcript_id attribute is required, so our GFF parser also expects it, while a gene_id attribute, though not strictly required by our GFF parser, is very useful for grouping alternative transcripts under a gene/locus identifier. An optional gene_name attribute, if found, will be taken and shown as  a symbolic gene name or short-form abbreviation (e.g. gene symbols from HGNC or Entrez Gene). Some annotation sources (e.g. Ensembl) place a "human readable" gene name/symbol in the gene_name attribute, like a HUGO symbol (while gene_id might be just an automatically generated numeric identifier for the gene).

Most bioinformatics programs generally expect at least the exon features which are enough to define the overall transcript structure, with optional CDS features to specify the coding segments. Our GFF reader will ignore redundant features like start_codon, stop_codon when whole CDS features were provided, and similarly UTR features are ignored when whole exon features were given. However, it is still possible to provide only CDS and *UTR features and our GFF parser will reassemble the exonic structure accordingly (internally converting these segments to exon segments).

Example of a GTF2 transcript record with minimal attributes:

20	protein_coding	exon	9873504	9874841	.	+	.	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	CDS	9873504	9874841	.	+	0	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	exon	9877488	9877679	.	+	.	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	CDS	9877488	9877679	.	+	0	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	exon	9888412	9888586	.	+	.	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	CDS	9888412	9888586	.	+	0	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	exon	9891475	9891998	.	+	.	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";
20	protein_coding	CDS	9891475	9891995	.	+	2	gene_id "ENSBTAG00000020601"; transcript_id "ENSBTAT00000027448"; gene_name "ZNF366";

GTF output from bioinformatics programs can also include an additional transcript feature line acting as a parent feature for the exon and CDS features which define the transcript structure and have the same transcript_id attribute. This is not required by the GTF2 specification (and makes such files more similar to GFF3, which always have a "parent" feature, see below) but may be useful for holding the global attributes of each transcript (instead of having them duplicated for each exon feature).

GFF3 files

As defined by the GFF3 specification, the parent features (usually transcripts, i.e. "mRNA" features) are required to have an ID attribute, but here again an optional gene_name attribute can be used to specify a common gene name abbreviation. If gene_name is not given, it can be also inferred from the Name or ID attributes of the parent gene feature of the current parent mRNA feature (if given in the input file). CDS and exon features are required to have a Parent attribute whose value must match the value of the ID attribute of a parent transcript feature (usually a "mRNA" feature).

Example of a GFF3 transcript record with minimal attributes:

ctg123	example	mRNA	1300	9950	.	+	.	ID=t_012143;gene_name=EDEN
ctg123	example	exon	1300	1500	.	+	.	Parent=t_012143
ctg123	example	exon	3000	3902	.	+	.	Parent=t_012143
ctg123	example	CDS	3301	3902	.	+	0	Parent=t_012143
ctg123	example	exon	5000	5500	.	+	.	Parent=t_012143
ctg123	example	CDS	5000	5500	.	+	1	Parent=t_012143
ctg123	example	exon	7000	9000	.	+	.	Parent=t_012143
ctg123	example	CDS	7000	7600	.	+	1	Parent=t_012143
ctg123	example	exon	9400	9950	.	+	.	Parent=t_012143

Feature restrictions

For various reasons our GFF parser currently assumes the following limits (maximum values) for the genomic length (span) of gene and transcript features:

• genes and transcripts should not span more than 7 Megabases on the genomic sequence
• exons should not be longer than 30 Kilobases
• introns should not be larger than 6 Megabases

Also, transcript IDs are expected to be unique per GFF input file (though we relaxed this restriction by limiting it to a chromosome/contig scope).