bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

, the general feature format (gene-finding format, generic feature format, GFF) is a

file format A file format is a standard way that information is encoded for storage in a computer file. It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary or free. Some file formats ...

used for describing

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s and other features of DNA,

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

sequences.

GFF Versions

The following versions of GFF exist:
General Feature Format Version 2
generally deprecated *

a derivative used by Ensembl
Generic Feature Format Version 3
*
Genome Variation Format
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 (GFF2, GFF3 and GTF) 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:

The 8th field: phase of CDS features

Simply put, CDS means "CoDing Sequence". The exact meaning of the term is defined by Sequence Ontology (SO). 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 (full list of meta data types can be found a
Sequence Ontology specifications
.

GFF software

Servers

Servers that generate this format:

Clients

Clients that use this format:

Validation

The

modENCODE The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome. ENCODE also supports further biomedical research by "generating community resources of genomics data, software, ...

project hosts a
online GFF3 validation tool
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. A
online validation service
is also available.

References

{{DEFAULTSORT:General Feature Format Computer file formats Bioinformatics