FASTA loves the first token
Many tools treat the first word after > as the unique ID; everything after the first space is just description—and often gets chopped.
Header etiquette
FASTA, DNA & Protein Sequence Cleaner and Validator
Paste FASTA, DNA, RNA, or protein sequence data to remove headers, line numbers, spaces, hidden formatting, and invalid characters. Validate strict DNA, IUPAC DNA, RNA, or protein residues, then copy or download clean output.
Input & Options
0 bases
Cleaning
Case conversion
Validation
DNA/RNA mode
Protein extras
Output Format
Cleaned & Validated
Your cleaned and validated sequence will appear here.
Tips: Ctrl/Cmd + K focuses the input. Validation updates as you type.
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FASTA Cleaner: Remove Headers and Extract Sequences
Release Updates
- Retargeted the page title and heading around FASTA, DNA & protein sequence cleaning.
- Added RNA validation support with strict ACGU and IUPAC RNA modes.
- Added a clearer use-case promise for cleaning FASTA, DNA, RNA, and protein sequence data.
- Added exact-match guide sections for FASTA cleaning, DNA cleaning, protein validation, IUPAC validation, and cleaning steps.
- Added a dirty-vs-clean example table covering FASTA headers, line numbers, IUPAC DNA, RNA, and protein stop symbols.
- Added DNA validation modes: Strict ACGT or IUPAC ambiguity-code support.
- Added precise error localization with first invalid character, position, and local sequence context.
- Added multi-FASTA processing with per-record pass/fail reporting.
- Added output controls for plain/FASTA export, wrap widths (60/70/80), and header preservation.
- Added a sequence summary panel with length, GC stats, ambiguous-base count, and warnings.
- Added protein extras toggle support for X, *, U, and O, plus residue frequency table.
Use this FASTA cleaner to remove header lines that begin with > and extract the sequence text underneath.
Multi-FASTA input is supported, so each record can keep its own header for FASTA output or be combined into plain cleaned
sequence output. This is useful when a database export includes long descriptions, accession text, or wrapped sequence lines
that need to be cleaned before BLAST, alignment, primer design, or classroom analysis.
DNA Sequence Cleaner: Remove Numbers, Spaces, and Invalid Characters
DNA sequence data often arrives with line numbers, spaces, tabs, copied PDF artifacts, or notes mixed into the bases. The
cleaner removes numeric prefixes at the start of lines and can remove all whitespace to produce one continuous sequence.
Choose strict DNA validation to allow only A, C, G, and T, or use IUPAC
mode when ambiguity codes such as N, R, and Y are expected.
Protein Sequence Cleaner: Validate Amino Acid Codes
Protein sequences use single-letter amino acid codes. In protein mode, the validator accepts the 20 standard residues by
default and can optionally allow X for unknown residues, * for stop, and the rare amino acids
U and O. The summary table counts residues so you can quickly spot unexpected symbols or unusual
composition before using the sequence downstream.
Sequence Validator: Strict DNA vs IUPAC Codes
Strict DNA mode is best when a tool expects only the four canonical DNA bases. IUPAC mode is better for consensus sequences,
degenerate primers, mixed reads, and database records that intentionally include ambiguity codes. RNA validation is also
available for A, C, G, and U, with IUPAC RNA mode accepting ambiguity
codes that use U instead of T. When validation fails, the tool reports the first invalid character,
its position, and nearby context.
How to Clean a FASTA Sequence
- Paste the FASTA, DNA, RNA, or protein sequence into the input box.
- Keep Remove FASTA headers & line numbers enabled to strip
>header lines and numeric prefixes. - Keep Remove all whitespace enabled to remove spaces, tabs, and line breaks.
- Choose uppercase or lowercase output if your next tool requires a specific case.
- Select strict DNA, IUPAC DNA, RNA, or protein validation to check the cleaned sequence.
- Copy the cleaned output or download it as plain text or FASTA.
Examples of Dirty vs Clean Sequence Input
| Problem | Dirty input | Cleaned output |
|---|---|---|
| FASTA header | >gene1 description
ATCG |
ATCG |
| Line numbers | 1 ATG CGT 60 |
ATGCGT |
| IUPAC DNA | ATGNNRY |
Valid in IUPAC mode |
| RNA | AUG CCG UUA |
AUGCCGUUA |
| Protein | MVLSPADKTN* |
Valid if stop * enabled |
All cleaning and validation runs locally in your browser. Your sequence data is not uploaded to a server.
5 Fun Facts about Cleaning Sequences
Invisible hitchhikers
Copying from PDFs can add non-breaking spaces or soft hyphens that look empty but break downstream parsers—cleaning nukes those ghosts.
Hidden artifacts
Lowercase is sometimes a signal
Genome browsers often lowercase repeats or low-complexity regions; changing case can erase that “masked” hint, so convert consciously.
Repeat masking
Rare amino letters exist
Selenocysteine (U) and pyrrolysine (O) appear in a few organisms, so this validator keeps them optional instead of allowing them by default.
Edge residues
GC clamps grip primers
Ending primers with a G/C boosts 3′ stability; tidy, whitespace-free sequences make it easier to spot a solid clamp and avoid miscounts.
Primer savvy