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GFF3 Sequences Extractor

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

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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.
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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.

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