GFF

From BioPerl

Contents 1 Description 2 GFF2 3 GTF 4 GFF3 5 Example

Description

GFF - The acronym originally stood for Gene Finding Format, but current specifications are using Generic Feature Format. GFF is a line based, tab separated format for storing features and annotations. This makes it simple to read and write.

See examples/tools/gb_to_gff.pl for an example of writing a GFF file from a Bio::Seq object.

GFF2

GFF2 specifications are available at the Sanger web site.

See Bio::DB::GFF, Bio::DB::SeqFeature, Bio::Tools::GFF, and Bio::SeqIO.

GTF

See the GTF page for more information. This is sometimes called GFF2.5 and was primarily developed for gene features.

GFF3

Version 3 is the most recent GFF specification (February 2007). A GFF3 validator is here and the GFF3 page has more info.

http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

Example

mmscl	supported_mRNA	CDS	40759	41225	.	+	.	Sequence "mmscl"
mmscl	supported_mRNA	exon	61468	61729	.	+	.	Sequence "mmMAP_17"
mmscl	supported_mRNA	exon	63653	63768	.	+	.	Sequence "mmMAP_17"
mmscl	supported_mRNA	exon	65434	65537	.	+	.	Sequence "mmMAP_17"
mmscl	supported_mRNA	exon	65983	66383	.	+	.	Sequence "mmMAP_17"
mmscl	RepeatMasker	Repeat	55	115	378	-	.	Target "B4" (230) 61 ; SINE/B4
mmscl	RepeatMasker	Repeat	160	304	1153	+	.	Target "B1_MM" 1 147 ; SINE/Alu