TXT to FASTA converter

How to convert TXT to FASTA?

Paste raw DNA, RNA, or protein text into the TXT to FASTA converter, or upload a text file, then download the resulting .fasta file. The converter accepts up to 10 million characters, removes copied line numbers and spacing, validates sequence characters, and creates or preserves FASTA headers. Sequence data stays on your device, and no account is required.

Choose how the input lines represent records before converting: Auto-detect sequences treats each non-empty raw sequence line as a separate record. For one sequence wrapped across several lines, select Join all lines into one sequence. For several wrapped sequences separated by blank lines, choose Split on empty lines. Existing FASTA headers preserve record boundaries in every mode. Load the One wrapped DNA sequence or Multiple protein sequences example to try these settings.

Two-column tables are supported too: rows shaped like seq_id<TAB>sequence or seq_id,sequence become FASTA records whose headers come from the first column, so spreadsheet exports convert cleanly. Files copied from Windows tools are handled as well, including UTF-8 byte order marks and non-breaking spaces.

For one sequence, the result contains one FASTA record:

>seq_1
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG

While for multi-sequence FASTA files, each sequence gets a new line:

>seq_1
ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG
>seq_2
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF

For multiple sequences, separate entries with blank lines, existing FASTA headers, or the selected custom separator. The output keeps each sequence as a separate FASTA record so it can be used in alignment tools, sequence search tools, or downstream bioinformatics pipelines.

How to use TXT to FASTA converter

ProteinIQ's TXT to FASTA converter works in your browser and requires no account or payment.

Inputs

Paste the sequence text into the input field or upload a file containing your raw sequences or existing FASTA records.

Settings

Check Multi-sequences first: the default works for separate raw sequences written one per line, while a single wrapped sequence needs Join all lines into one sequence. Then adjust headers, cleanup, or output wrapping if your workflow requires it.

Results

The converter produces FASTA-formatted output that can be copied to clipboard or downloaded as a .fasta file. The final Logs tab shows conversion settings, sequence statistics, cleanup totals, and detailed cleanup or validation messages. The same run.log remains downloadable from Files.

How to make a FASTA file from a TXT file

While using ProteinIQ's TXT to FASTA converter is the simplest way, you can also convert a plain text file to FASTA manually by adding a header line that starts with > and placing the sequence on the next line. This is the standard way to create a FASTA file from raw sequence text before saving it with a .fasta or .fa extension.

Edit the file in a text editor

For small files, open the .txt file in a plain text editor such as Notepad or TextEdit and format each sequence like this:

>Sequence_1
MTEITAAMVKELRESTGAGMMDCKNALSETQHEWAYK

If your file contains multiple sequences, repeat the same pattern for each entry:

>Sequence_1
MTEITAAMVKELRESTGAGMMDCKNALSETQHEWAYK
>Sequence_2
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF

How to save a FASTA file

After formatting the header and sequence lines, use Save As in a text editor and save the file as plain text with a .fasta or .fa extension. If the editor appends .txt, choose plain text output explicitly and rename the file so the final filename ends in .fasta or .fa.

Use a converter when the input is messy

If the text contains numbering, spaces, or inconsistent formatting, use a dedicated converter to clean the sequences and generate headers automatically. ProteinIQ supports pasted text and uploaded files, so it is useful when manual editing would be slow or error-prone.

FASTA format rules

FASTA files are simple, but a few rules matter for downstream tool compatibility.

• Header line: Each sequence starts with a single header line beginning with >. The identifier should be unique within the file.
• Sequence line: Put the sequence directly below the header. Many tools accept wrapped lines, but one continuous line per sequence is often easier to inspect.
• Valid characters: Use standard nucleotide codes such as A, C, G, T, U, and N, or standard one-letter amino acid codes for proteins.
• Alignment gaps: Gapped alignment FASTA files may contain - or . gap characters. Enable Preserve alignment gaps when converting aligned sequences.
• Protein stops: Translated protein FASTA records sometimes end with * to mark a stop codon. Enable Preserve stop codons if you need to keep that terminal marker.
• No numbering or spaces: Remove residue numbers, tabs, spaces, and other non-sequence characters unless a tool explicitly allows them.
• Plain text file: Save the file as plain text before renaming it to .fasta or .fa.

Which FASTA converter should I use?

Use TXT to FASTA when your input is a plain text sequence, copied sequence block, or .txt file. Use a more specific converter when the source file has a structured format with metadata or quality scores.

FAQ

How do I convert a text file to FASTA format?

Upload the .txt file or paste its contents, choose DNA, RNA, Protein, or Auto-detect, and run the converter. The result can be copied or downloaded as a .fasta file with headers and wrapped sequence lines.

How do I save a TXT file as FASTA?

Add a header line that starts with > above each sequence, put the sequence on the next line, and save the file as plain text with a .fasta or .fa extension. If your editor appends .txt, rename the file so it ends in .fasta or .fa. This converter can generate the headers and the downloaded file for you.

What characters are valid in DNA, RNA, and protein FASTA?

DNA uses A, C, G, T, and ambiguity codes such as N, R, and Y. RNA uses U in place of T. Protein uses one-letter amino acid codes such as A, C, D, E, and M, plus ambiguity and extended codes such as X, B, Z, J, O, and U.

Can FASTA contain gaps?

Yes. Aligned FASTA files often contain - or . gap characters to keep homologous positions in the same columns, while raw unaligned FASTA usually should not. Enable Preserve alignment gaps when your input is already an alignment.

How do I convert a sequence that spans multiple lines?

Choose Join all lines into one sequence under Multi-sequences, or Split on empty lines if your file separates records with blank lines. Auto-detect treats every raw line as its own record, which suits lists of short sequences but would split one wrapped sequence into pieces. Input that starts with > headers is unaffected because each FASTA record always stays whole.

What happens to duplicate sequence names?

If two records produce the same header, the converter appends _2, _3, and so on to later duplicates so every identifier in the output FASTA stays unique.

Should I use TXT to FASTA or FASTQ to FASTA?

Use TXT to FASTA for raw sequences copied from notes, spreadsheets, or plain text files. Use FASTQ to FASTA when your input is sequencing-read data, since FASTQ includes quality-score lines that need a dedicated converter to strip.