Opening a GFF3 File

The GFF3 file type is primarily associated with AUGUSTUS.

GFF3	File extension: GFF3
	File type:	annotation file

What is a GFF3 file

GFF3 files mostly belong to AUGUSTUS. GFF3 files keep genome annotations in a tab-separated text format. Each line describes a genomic feature, such as a gene, mRNA, exon, or CDS, with clear coordinates and attributes.
The file structure contains several fields: the sequence name, the source of the annotation, the feature type, the start and end positions, and an additional column for detailed attributes.

Annotation Details: Each record specifies the location and type of gene feature.
Standardized Format: The consistent, tab-delimited layout allows for easy parsing and integration with other tools.
Tool Integration: Programs like AUGUSTUS, GenomeHubs, and GenomeTools utilize this format for genome annotation. Some files may be compressed using GZIP for storage efficiency.

FilExt.com note: For more on the formal guidelines, visit the AUGUSTUS webpage or the Sequence Ontology site.

How to open GFF3 files

You need a suitable software like AUGUSTUS to open a GFF3 file. Without proper software you will receive a Windows message "How do you want to open this file?" or "Windows cannot open this file" or a similar Mac/iPhone/Android alert. If you cannot open your GFF3 file correctly, try to right-click or long-press the file. Then click "Open with" and choose an application. You can also display a GFF3 file directly in the browser:. Just drag the file onto this browser window and drop it.

Online GFF3 Text Viewer

Choose your .gff3 file to view

or drag and drop it here

Online File Viewer

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How to extract texts from GFF3 files or capture a screenshot to PDF, JPG, DOCX, TXT, ...

If you want to extract texts from GFF3 file or capture a screenshot, you can use our free Online GFF3 File Viewer:

Just click the "Choose your .gff3 file to view" button on this page.
After your file is opened in browser,
click "Save as..." in the menu.
Then choose the file format (e.g. JPG, PDF, DOCX, TXT, ...) you want.
Your file will be converted and downloaded.

Programs that open and convert GFF3 files:

AUGUSTUS
See the previous paragraphs to learn more about the main application. GFF3 files are often referred to as AUGUSTUS data files because this type of file is primarily created or used by this software.
Integrated Genome Browser
GFF3 stands for General Feature Format. This file format is used to store genomic data that describes genes and other features of DNA, RNA and protein sequences. Genome browsers are special software that provide a graphical interface for users to display genomic data. GFF3 files can be accessed using several genome browsers including GBrowse, Integrated Genome Browser (IGB) and Jalview.

GFF3 format details:

Why is it important to know the file format? This is the only way to find out which program to use to open the file. The first characters in a file identify the file format, for example, HTML files start with the bytes <html>. If the file extension does not match the file format, double-clicking on the file will cause an error upon opening. Exact knowledge of the format is therefore important in order to solve problems occurring in files. In the following you will find our evaluation of the GFF3 files:

Files with the GFF3 extension are quite widely used. This file type is mainly used by one program with a specific format. However, the following two file formats are common:

75% of all GFF3 files belong to Generic Feature Format Version 3. These files are plain text, which means they can be viewed with any text editor such as Windows Editor, Nano for Linux, and TextEdit for macOS. The files are often between 950 bytes and 95 MB in size. The file type is relatively new. Certain words are almost always found in the files, such as ##gff-version 3, sequence, region, Name and NCBI. Such files are related to genes, annotation, release, ncbi, sapiens, homo, gene and grch.
8% of all GFF3 files start with the magic bytes ##sequence-region, which are always the first bytes of this file format. The content consists of readable text data, which can be read using a text editor. Most of these files are 660 bytes to 7 MB in size. The keywords sequence, Dbxref, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi, region, species https, taxon and RefSeq are typical for these files. The file name sequence.gff3 is typical for these files.

All other GFF3 files (17%) have no consistent format, the following 5 formats exist: GZIP and chr. These files are often connected to variants, gencode, vibrio, output, chromosome or cholerae. Just click the "Choose your .gff3 file to view" button on this page to find out what your GFF3 file is.

Technical Data for GFF3 File Extension

File classification:

Data

Related files:

gtf, gff2, bed, fasta, vcf, gff, fa, gz, bed, fna, zip, gbf, uxd, out, gb, nii, dat, pkl, lic

Mime type:

text/plain

a gff3 annotation file is a special file format and should only be edited and saved with the appropriate software.

How to solve problems with GFF3 files

Associate the GFF3 file extension with the correct application.
Update your software that should actually open annotation files. Because only the current version supports the latest GFF3 file format. Search, therefore, e.g. on the manufacturer website after an available AUGUSTUS update.
To make sure that your GFF3 file is not corrupted or virus-infected, get the file again and scan it with Google's virustotal.com.
Click here to open your .GFF3 file online - secure, fast, and no downloads needed.