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

File format

A file format is a particular way that information is encoded for storage in a computer file.Since a disk drive, or indeed any computer storage, can store only bits, the computer must have some way of converting information to 0s and 1s and vice-versa. There are different kinds of formats for...

 used for describing gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s and other features of DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

, RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 and protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 sequences. The filename extension

Filename extension

A filename extension is a suffix to the name of a computer file applied to indicate the encoding of its contents or usage....

 associated with such files is .GFF.

There are two versions of the GFF file format in general use:

• General Feature Format Version 2 (Sanger Institute)
• Generic Feature Format Version 3 (Sequence Ontology Project)

Servers that generate this format:
! Server !! Example file
|-
| Expasy

ExPASy

ExPASy is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences...

 >

http://www.uniprot.org/uniprot/P0A7B8.gff >-

Clients that use this format:

Name	Description	Links
GBrowse	GMOD genome viewer	GBrowse
IGB	Integrated Genome Browser	Integrated Genome Browser Integrated Genome Browser Integrated Genome Browser is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.- History :...
Jalview	A multiple sequence alignment editor & viewer	Jalview Jalview Jalview is a multiple sequence alignment editor and viewer written in the Java programming language. The programme was originally written by Michele Clamp whilst working in Geoff Barton's group at the EBI....
STRAP	Underlining sequence features in multiple alignments. Example output: http://www.charite.de/bioinf/strap/exampleOutput.html	http://3d-alignment.eu/

GFF Versions

GFF Version 2 has 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 Gene transfer format

Gene transfer format

The Gene transfer format is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format , but contains some additional conventions specific to gene information. A significant feature of the GTF is that it is validatable:...

 (GTF) is a refinement of GFF Version 2 and is sometimes referred to as GFF2.5.

Validation

The modENCODE project hosts an online GFF3 validation tool with generous limits.