Input EMBL
💡 Quick Summary
EMBL to FASTA accepts one or more EMBL records and returns the DNA sequence(s) in FASTA format, removing all annotation, feature table entries, and non-sequence data.
📋 How to Use
- Paste the contents of one or more EMBL files into the input area.
- Click Convert. Each record's DE (description) line becomes the FASTA title; the SQ section is extracted, cleaned, and wrapped to 60 characters per line.
- The Records Converted and Total Length stats update immediately.
- Use the Copy button to copy the FASTA output to your clipboard.
- Click Load Example to try the tool with a sample EMBL record.
- Click Clear to reset and start again.
🧮 Formulas & Logic
Title
FASTA title = first DE line content, with "" removed
Sequence
All non-IUPAC-DNA characters (spaces, digits, newlines) stripped from SQ block before // terminator
Wrapping
Sequence wrapped at 60 characters per line (addReturns)
📊 Result Interpretation
Records Converted
Number of EMBL records (ID … //) successfully converted. Each record produces one FASTA entry.
Total Length
Sum of all extracted DNA sequence characters across all converted records.
🔬 Applications
- Extracting bare DNA sequences from EMBL flat files for use in BLAST or alignment tools
- Converting downloaded ENA/EMBL records to FASTA for downstream bioinformatics pipelines
- Stripping annotation from EMBL files before loading sequences into a sequence editor
- Batch-converting multiple EMBL records into a single multi-FASTA file
⚠️ Common Mistakes & Warnings
Only the DNA sequence is extracted
Feature annotations (CDS, mRNA, gene coordinates), cross-references, and taxonomy information are discarded. Use the EMBL Feature Extractor tool if you need feature data.
Multi-line DE fields are truncated
Only the first DE line is used as the FASTA title. If the description spans multiple lines, subsequent lines are not appended.
Input size limit: 200,000,000 characters
This matches the original SMS limit. Very large whole-genome EMBL files may need to be split before processing.
❓ Frequently Asked Questions
Where can I get EMBL-format sequences?
EMBL flat files can be downloaded from the European Nucleotide Archive (ENA) at www.ebi.ac.uk/ena. Search for an accession number and choose the "EMBL" download format.
What is the EMBL flat file format?
EMBL format is a plain-text sequence format used by the European Molecular Biology Laboratory database. Each record begins with "ID " and ends with "//". The DE line holds the description; the SQ block holds the nucleotide sequence.
Can I paste multiple EMBL records at once?
Yes. Paste the full contents of an EMBL file containing any number of records. Each record is converted to a separate FASTA entry in the output.
What characters are kept in the sequence?
Only valid IUPAC DNA/RNA characters (A T G C U R Y S W K M B D H V N X) are retained. Spaces, digits, and formatting characters from the EMBL SQ block are stripped automatically.