💡 Quick Summary
GenBank to FASTA reads one or more GenBank flat-file records and returns each DNA sequence as a separate FASTA entry, using the DEFINITION line as the title. It is the fastest way to strip annotation text and obtain a clean sequence for tools like BLAST, alignment, or primer design.
📋 How to Use
- Paste the contents of one or more GenBank files into the input area. Each record must start with a LOCUS line and contain both a DEFINITION section and an ORIGIN section ending with
//. - Click Convert to FASTA. Each GenBank record is converted to a single FASTA entry; the DEFINITION line becomes the FASTA title.
- The Summary panel shows how many records were converted and the total number of bases extracted.
- Use the Copy button to copy all FASTA sequences to your clipboard.
- Click Load Example to try with a real GenBank record — the Strongylocentrotus purpuratus fascin (FSCN1) mRNA from NCBI.
- Click Clear to reset.
🧮 Formulas & Logic
📊 Result Interpretation
Number of GenBank records (LOCUS … //) successfully parsed and converted to FASTA.
Sum of all DNA characters extracted across all converted records, after stripping digits, spaces, and non-IUPAC characters from the ORIGIN block.
🔬 Applications
- Stripping GenBank annotation to obtain a bare FASTA sequence for BLAST submission
- Preparing sequences for multiple sequence alignment tools that require FASTA input
- Extracting full genomic sequences from downloaded GenBank files before primer design
- Batch-converting multiple GenBank records in a single paste operation
- Converting GenBank sequences to FASTA as a pre-processing step for bioinformatics pipelines
⚠️ Common Mistakes & Warnings
The tool reads only the sequence data between the ORIGIN header and the // terminator. Annotation sections (FEATURES, REFERENCE, etc.) are ignored entirely.
The ORIGIN section is cleaned with an IUPAC DNA filter. GenBank records where ORIGIN contains amino acids (rare) will produce an empty or incorrect sequence.
Only the DEFINITION section text is used for the FASTA header. If the record has no DEFINITION, the title will be blank. The ACCESSION or VERSION line is not appended automatically.
Records missing a DEFINITION, ACCESSION, or ORIGIN section cannot be parsed and are skipped with a warning.