GFF
Contents |
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://public.ecolihub.net/cgi-bin/validate_gff3_online/validate_gff3_online
The original WormBase GFF3 validator is currently offline.
Example
mmscl supported_mRNA CDS 40759 41225 . + . Parent=mmscl mmscl supported_mRNA exon 61468 61729 . + . Parent=mmMAP_17 mmscl supported_mRNA exon 63653 63768 . + . Parent=mmMAP_17 mmscl supported_mRNA exon 65434 65537 . + . Parent=mmMAP_17 mmscl supported_mRNA exon 65983 66383 . + . Parent=mmMAP_17 mmscl RepeatMasker Repeat 55 115 378 - . Target=B4;Note="(230) 61";Name="SINE/B4" mmscl RepeatMasker Repeat 160 304 1153 + . Target=B1_MM;Note="1 147";Name="SINE/Alu"
