General feature format

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The general feature format (gene-finding format, generic feature format, GFF) is a file format used for describing genes and other features of DNA, RNA and protein sequences. The filename extension associated with such files is .GFF and the content type associated with them is text/x-gff3.

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

Servers that generate this format:

Server Example file
UniProt [1]

Clients that use this format:

Name Description Links
GBrowse GMOD genome viewer GBrowse
IGB Integrated Genome Browser Integrated Genome Browser
Jalview A multiple sequence alignment editor & viewer Jalview
STRAP Underlining sequence features in multiple alignments. Example output: [2] [3]
JBrowse JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5 JBrowse.org
ZENBU A collaborative, omics data integration and interactive visualization system [4]

GFF Versions[edit]

GFF Version 2 (along with its more common GTF variant[1]) 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.

GFF general structure[edit]

All GFF formats (GFF2, GFF3 and GTF) are tabular files with 9 fields per line, separated by tabs. They all share the same structure for the first 7 fields, while differing in the content and format of the ninth field. The general structure is as follows:

General GFF structure
Position index Position name Description
1 sequence The name of the sequence where the feature is located.
2 source Keyword identifying the source of the feature, like a program (e.g. Augustus or RepeatMasker) or an organization (like TAIR).
3 feature The feature type name, like "gene" or "exon". In a well structured GFF file, all the children features always follow their parents in a single block (so all exons of a transcript are put after their parent "transcript" feature line and before any other parent transcript line). In GFF3, all features and their relationships should be compatible with the standards released by the Sequence Ontology Project.
4 start Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED files.
5 end Genomic end of the feature, with a 1-base offset. This is the same end coordinate as it is in 0-offset half-open sequence formats, like BED files.[citation needed]
6 score Numeric value that generally indicates the confidence of the source on the annotated feature. A value of "." (a dot) is used to define a null value.
7 strand Single character that indicates the Sense (molecular biology) strand of the feature; it can assume the values of "+" (positive, or 5'->3'), "-", (negative, or 3'->5'), "." (undetermined).
8 phase phase of CDS features; it can be either one of 0, 1, 2 (for CDS features) or "." (for everything else). See the section below for a detailed explanation.
9 Attributes. All the other information pertaining to this feature. The format, structure and content of this field is the one which varies the most between the three competing file formats.

The 8th field: phase of CDS features[edit]

Simply put, CDS means "CoDing Sequence". The exact meaning of the term is defined by Sequence Ontology (SO). According to the GFF3 specification[2][3]:

For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon.

Meta Directives[edit]

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 at Sequence Ontology specifications).

Validation[edit]

The modENCODE project hosts an 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. An online validation service is also available.

See also[edit]

References[edit]

  1. ^ "GTF2.2: A Gene Annotation Format".
  2. ^ "GFF3 specification".
  3. ^ http://gmod.org/wiki/GFF3