EMBL Feature Extractor

Extract sequence features (CDS, mRNA, exons, introns) from EMBL files and convert to FASTA format

What is EMBL Feature Extractor?

The EMBL Feature Extractor is a specialized tool that reads EMBL database files and extracts individual sequence features from the feature table (FT section). It converts each feature (CDS, mRNA, exon, intron) into FASTA format with the actual nucleotide sequence from the specified coordinates.

How to Use This Tool

Quick guide to extract features:

  1. Paste your EMBL file content or upload an EMBL file
  2. Features are automatically extracted and converted to FASTA
  3. Download or copy the extracted sequences

When to Use

This tool is essential when you need to:

  • Extract CDS sequences from genomic DNA for protein analysis
  • Obtain mRNA sequences without introns from genomic records
  • Extract individual exons or other annotated features
  • Convert EMBL feature table entries to analyzable FASTA sequences

Example Input

Sample EMBL format with features:

ID EXAMPLE; DNA; 100 BP. FT CDS 10..50 SQ Sequence 100 BP; atcgatcgat cgtagctacg tacgtagcta...

Try with your own EMBL file or click Example.

Example Output

Expected FASTA format output:

>EXAMPLE CDS 10..50 CGTAGCTACGTACGTAGCTATCGATCGATCGATCGATCGAT

Each feature becomes a separate FASTA entry.

FAQ

Q: What features can be extracted?
A: CDS, mRNA, exon, intron, gene, and all standard EMBL feature types.

Q: Does it handle complement/join locations?
A: Yes, it processes complement and simple join coordinates correctly.