FASTA validator
Find malformed FASTA records and invalid DNA, RNA or protein symbols with line and column diagnostics.
Checks a strict FASTA profile with one header line beginning with >, a unique first-token identifier and a nonempty sequence for each record. DNA and RNA use separate IUPAC alphabets. Protein accepts the standard amino acids plus B, X, Z, J, U, O and *. Lowercase is accepted. Empty lines are ignored; sequence whitespace, digits, comments, mixed T/U and unsupported symbols are reported with line and column. Optional gaps are literal -. This is format validation, not a GenBank submission check or biological quality assessment. Runs locally without uploads or database lookup. Limit: 500000 combined input characters, 2000 records, 2000 validation issues, a 1000-symbol motif, 20000 matches and 10000000 symbol comparisons. Exceeding a limit rejects the complete report. Each export is limited to 3000000 characters; typed CSV allows 200000 values. Preview shows 200 rows. Processing stops after 10 seconds. Up to 500,000 characters. Review the settings before running.
Your result
How to use FASTA validator
- Paste FASTA records and choose DNA, RNA or protein.
- Enable literal alignment gaps only if the input uses them.
- Review every issue and download the complete diagnostic report.
Useful next steps
Choose the alphabet explicitly
The validator never guesses sequence type or removes invalid characters. DNA uses T; RNA uses U. Protein validation checks symbols, not biological correctness.
Keep identifiers unique
The first token after > identifies a record. Full headers are preserved. This general FASTA profile does not certify GenBank submission requirements.