Any Onine Tool Logo
AnyOnlineTool Logo
Register

Existing customer? Login

GFF3 Sequences Extractor

Extract DNA or protein sequences from GFF3 annotation files by uploading GFF3 and corresponding FASTA files.

Request Feature / Support
5,752+
Total Calculations Run
< 15ms
Browser Execution Speed
100%
Client-Side Privacy
4.9 / 5.0
User Satisfaction
AI Web Tool Generator

Build Your Own Custom Web Calculator in Seconds

Type what tool or calculator you need below. Our AI will build it instantly for your site.

Popular ideas:
100% FREE • No Credit Card Required

About This Tool

The GFF3 Sequences Extractor is a specialized bioinformatics tool that allows researchers to extract DNA or protein sequences from GFF3 (General Feature Format version 3) annotation files. Upload your GFF3 file along with the corresponding FASTA sequence file, select the features you want to extract (genes, exons, CDS, etc.), and the tool will parse the GFF3 annotations, extract the corresponding sequences from the FASTA file, and provide them in downloadable FASTA format. This tool handles complex GFF3 structures including multi-line features, parent-child relationships, and reverse complement sequences.
Save your calculation history with a free account

How to Use

  1. Upload your GFF3 annotation file using the file upload area
  2. Upload your corresponding FASTA sequence file (DNA or protein)
  3. Select the feature types you want to extract (genes, mRNAs, exons, CDS, etc.)
  4. Choose extraction options: include reverse complement for features on minus strand, include feature attributes in FASTA headers
  5. Click 'Extract Sequences' to process the files
  6. View the extracted sequences in the results panel and download as FASTA file
How to use gff3 sequences extractor

Frequently Asked Questions

Find Quick Answers

What is a GFF3 file?
GFF3 (General Feature Format version 3) is a standard file format for storing genomic annotations. It describes features like genes, exons, mRNAs, and their locations on reference sequences.
Do I need both GFF3 and FASTA files?
Yes, the GFF3 file contains annotation coordinates, while the FASTA file contains the actual DNA or protein sequences. The tool uses coordinates from GFF3 to extract corresponding sequences from the FASTA file.
What sequence formats are supported?
The tool extracts sequences in standard FASTA format. Input FASTA files can contain DNA or protein sequences. The output will be in FASTA format with customizable headers.
Can I extract specific feature types?
Yes, you can select which feature types to extract (genes, mRNAs, exons, CDS, etc.). The tool automatically detects all feature types present in your GFF3 file.
Is there a file size limit?
The tool processes files entirely in your browser, so performance depends on your device's memory. For very large genomic files (hundreds of MB), consider splitting them into smaller chunks.

Need to run multiple calculations?

Create a free account today to unlock unlimited daily runs, access advanced parameters, save your history, and request custom features.

Register Free Account

Related Tools

Other useful calculators and utilities you might like

Science Tools

Spotify to MP3 Converter

Convert Spotify tracks and playlists to MP3 format instantly with our free online converter.

Science Tools

Road Distance Calculator

Calculate the driving distance and travel time between two addresses with our free online road dista...

Science Tools

Age Calculator

Calculate your exact age in years, months, and days from any birth date to any target date.

Science Tools

Currency Converter

Convert currencies instantly with real-time exchange rates and historical data support.

Your Feedback Matters

Help Us to Improve