Sequence Cleaner & Validator (DNA/Protein, FASTA)

How It Works:

This scientific sequence cleaner and validator is a simple way to prepare DNA or protein sequences for analysis. It helps you turn messy input into a clean, consistent string of letters that bioinformatics tools can read. If you are copying sequence data from a PDF, a lab notebook, or a FASTA file, small formatting issues can cause errors. This calculator fixes those problems quickly and clearly, right in your browser.

A sequence is just a string of letters, but those letters must follow rules. DNA sequences are made of A, C, G, and T, while protein sequences use the 20 standard amino acid single-letter codes. The validator checks that your sequence contains only the letters that belong to the type you select. If an unexpected character appears, you will see an error so you can correct it before running downstream tools like alignment, translation, or primer design.

Cleaning focuses on removing formatting noise. Many FASTA files include header lines that start with a greater-than symbol and descriptive text. Some sources add line numbers, spaces, tabs, or line breaks. These extras are helpful for humans but can break software that expects a clean string. The cleaner removes those extras so the sequence is ready for copy-paste into BLAST, primer checkers, or lab software.

Cleaning:

• Remove FASTA headers and line numbers: Strips any header lines that begin with > and any numeric prefixes that appear at the start of a line.
• Remove all whitespace: Deletes spaces, tabs, and line breaks so you get one continuous sequence string.

Validation:

The validator checks your sequence against the allowed alphabet for the selected type:

• DNA (ACGT): Accepts only A, C, G, and T (case-insensitive).
• Protein (20 AAs): Accepts the standard amino acid letters A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y (case-insensitive).

To use the tool, paste your sequence into the input area, choose DNA or protein, and select the cleaning options you need. The output updates instantly, so you can confirm the cleaned result and copy it into your next workflow step. Because all processing happens locally, your sequence data stays private and never leaves your device.

Common use cases include cleaning a FASTA sequence for a student assignment, validating a PCR product sequence before ordering primers, checking amino acid strings from a protein database, or preparing input for a multiple sequence alignment. It is also useful when you are troubleshooting a pipeline and need to verify that hidden characters or formatting issues are not the cause of an error.