FASTA Validator and Converter
Free online FASTA validator and converter. Paste or upload a FASTA or multi-FASTA file to check its formatting, get sequence statistics, then clean, rewrap and convert it to CSV, TSV or plain sequences, directly in your browser.
What this FASTA validator and converter does
Paste or upload a FASTA or multi-FASTA file to check it for structural problems and get instant statistics: number of sequences, total, minimum, maximum and average length, and GC content for nucleotide data. The tool automatically detects whether the file contains nucleotide or protein sequences, lists every issue found by severity (error, warning, info) and shows a per-sequence table with ID, description and length. Everything runs locally in your browser: files are read with the File API and never uploaded.
What the validator checks
The validator flags sequence data placed before the first header line, empty headers, records without sequence, duplicate identifiers, invalid characters for the detected alphabet (IUPAC nucleotide codes or amino acid codes), spaces or digits inside sequences, blank lines in the middle of a record, lowercase residues, inconsistent line widths and Windows (CRLF) line endings. These are common causes of parsing errors in downstream bioinformatics tools.
Cleaning and conversion options
Rewrap sequence lines to 60, 70 or 80 characters (or write each sequence on a single line), convert to uppercase, remove gap characters, strip trailing stop symbols (*) and drop empty records. Export the result as clean FASTA, CSV, TSV, a plain list of sequences or a list of headers, and optionally apply a transformation to nucleotide sequences: complement, reverse complement, reverse, DNA to RNA (T to U) or RNA to DNA (U to T). Copy the output or download it as a file.
FASTA Format Validator & Converter
Paste or upload a (multi-)FASTA file to check it for formatting problems, get sequence statistics, then clean, rewrap or convert it to CSV, TSV or plain sequences — all in your browser.
Validation report
Sequences
Clean & convert
All processing happens locally in your browser — uploaded files are read with the File API and never sent to a server. Sequence type is auto-detected (nucleotide if at least 90% of residues are IUPAC nucleotide codes, otherwise protein). Validation checks structure and alphabet only; it does not verify biological correctness of a sequence.
FAQ
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What is the FASTA format?
FASTA is a plain-text format for nucleotide or protein sequences. Each record starts with a header line beginning with the greater-than sign (>) followed by an identifier and an optional description, then one or more lines of sequence. A file containing several records is called a multi-FASTA file. -
What errors does the FASTA validator detect?
It detects sequence data before the first header, empty headers, records with no sequence, duplicate identifiers and invalid characters for the detected sequence type. It also reports spaces or digits inside sequences, blank lines within a record, lowercase residues, inconsistent line widths and Windows line endings, each labeled as an error, warning or information. -
How does the tool decide whether a file contains DNA/RNA or protein?
It pools all residues in the file and counts IUPAC nucleotide codes (A, C, G, T, U, N, R, Y, K, M, S, W, B, D, H, V) together with gap and stop symbols. If at least 90% of residues belong to that set, the file is treated as nucleotide, otherwise as protein. Very short peptides made mostly of A, C, G and T residues can occasionally be misclassified as nucleotide. -
How do I convert a FASTA file to CSV or TSV?
Paste or upload the file, choose CSV or TSV in the output format menu, then copy or download the result. Each sequence becomes one row with its ID, description, length and sequence, ready to open in Excel, R or pandas. -
What line width should I use for FASTA sequences?
The FASTA format does not mandate a line width and most tools accept any length. Common conventions are 60, 70 or 80 characters per line, while some pipelines prefer each sequence on a single line. The converter supports all of these so you can match what your downstream software expects. -
Is my file uploaded, and how large a file can I process?
No. The file is read locally in your browser and never sent to a server. Typical sequence sets, gene panels and protein collections process instantly, but very large files such as whole genomes may be slow or exhaust browser memory. For those, command-line tools such as SeqKit or Biopython are better suited.