FASTA Formatter and Sequence Cleaner

Clean, validate, reformat, convert, and print biological sequences.

How to use this tool

Paste raw sequence text or load a text-based sequence file. Choose the alphabet and cleanup rules, then select plain text, FASTA, or printable dsDNA output.

Conservative by default: Spaces and digits are removed, but unexpected biological characters are kept and reported.
FASTA formatting: Preserve or generate headers and wrap each record at a standard or custom line width.
Alphabet validation: Validate DNA, RNA, protein, IUPAC ambiguity codes, gaps, and protein stop symbols.
Printable dsDNA: Display aligned 5′ and 3′ strands with complements, blocks, base ranges, and pairing bars.

1 · Input Sequence

Sequence text or FASTA

Records: 0Output characters: 0Input: —

Try an example:

Accepts up to 1,000,000 cleaned sequence characters, 1,000 records, and 1,000 characters per FASTA header.

2 · Cleanup and Validation

Remove whitespace and line breaksRemove digits and line numberingRemove alignment gaps (- and .)Unexpected charactersLetter caseDNA / RNA conversion

3 · Output Format

Line width (0 = unwrapped)Preserve existing headersGenerated header prefix

4 · Cleaned Result

0 records0 characters

Change report

No cleanup changes were applied.

DNA · RNA · Protein · IUPAC · Multi-FASTA · Browser-private

How sequence cleaning and FASTA formatting work

What does a sequence cleaner remove?

Sequence text copied from papers, GenBank-style displays, PDFs, email, or lab documents often contains spaces, line numbers, inconsistent case, and hidden line endings. Conservative cleanup removes known formatting artifacts while leaving unexpected characters visible for review.

What is FASTA formatting?

Each FASTA record begins with a single header line starting with >, followed by one or more sequence lines. Line wrapping changes readability but not the biological sequence. Common widths include 60, 70, and 80 characters.

Why are unsupported characters reported?

Silently deleting an unexpected character can alter a biological sequence. This tool therefore keeps and reports unsupported characters by default. Removal or replacement with N for nucleic acids or X for proteins requires an explicit selection.

What is printable dsDNA?

The dsDNA view displays the entered strand 5′ to 3′ and its complementary strand antiparallel from 3′ to 5′. It is a readable presentation format, not a FASTA representation.