TXT to FASTA converter

How to convert TXT to FASTA?

To convert a TXT file to FASTA, give every sequence a header line that starts with > followed by its name, put the sequence on the lines below, and save the file as plain text with a .fasta extension. You can do it online with this converter, by hand in a text editor, or with an awk one-liner on the command line.

Online with the TXT to FASTA converter

The converter finds sequence names, joins wrapped lines, strips copied numbering and spacing, and writes one FASTA record per sequence. It runs in your browser, and no account is needed.

1. Paste your sequences into Text input, or click Files and upload a .txt, Word (.docx), or PDF file.
2. Check the FASTA preview on the right. It updates as you type, with a summary of how many sequences were found.
3. Read any notice above the preview. If one sequence was split into several records, set Multi-sequences to Join all lines into one sequence.
4. Click Download FASTA, or copy the preview.

Manually in a text editor

1. Open the .txt file in Notepad, TextEdit, or any plain text editor.
2. Add a line above each sequence that starts with > and a short name, such as >primer_F. Leave no space after the >.
3. Delete any numbers, spaces, and blank lines inside each sequence.
4. Save as plain text with a .fasta or .fa extension. In Notepad, set Save as type to All files so the name doesn't become sequences.fasta.txt; in TextEdit, choose Format, then Make Plain Text first.

primer_F ATGGATTTATCTGCTCTTCG
primer_R CTAAGATTTTCTGCATAGCA

>primer_F
ATGGATTTATCTGCTCTTCG
>primer_R
CTAAGATTTTCTGCATAGCA

Renaming sequences.txt to sequences.fasta without adding the > lines does not make a FASTA file. Most programs reject it, because the header line is what marks where each record starts.

On the command line with awk

When each line holds a name and a sequence separated by a space or tab, as in the input above, this awk command writes the same FASTA output:

awk '{ printf ">%s\n%s\n", $1, $2 }' sequences.txt > sequences.fasta

For a file with one unnamed sequence per line, number the records instead. Two lines of sequence become >seq_1 and >seq_2:

awk '{ printf ">seq_%d\n%s\n", NR, $0 }' sequences.txt > sequences.fasta

Both commands assume one complete sequence per line. They don't join wrapped sequences, strip position numbers, or keep a name that contains spaces, and a file saved on Windows needs its carriage returns removed first with tr -d '\r' < sequences.txt > clean.txt. Text copied from a database or a paper usually breaks at least one of these assumptions, which is where the converter above is faster.

Examples

A name line above a sequence becomes the FASTA header, and a sequence wrapped over several lines stays one record:

Human insulin
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKT
RREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

>Human_insulin
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPL
ALEGSLQKRGIVEQCCTSICSLYQLENYCN

Several named sequences become a multi-FASTA file. Blank lines between them are optional:

GFP
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT

mCherry
MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKL

>GFP
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTT
>mCherry
MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKL

Text copied from GenBank, UniProt, or a paper keeps its position numbers and 10-residue blocks. Those are removed and the lines are joined:

BRCA1 fragment
        1 atggatttat ctgctcttcg cgttgaagaa gtacaaaatg tcattaatgc
       51 tatgcagaaa atcttagagt

>BRCA1 fragment
ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGT

A line with one sequence and no name, such as a list of primers or peptides, becomes one record per line (>seq_1, >seq_2, and so on). Spreadsheet columns work too. Headers such as name and sequence identify the columns, even when a name or note could also be read as amino acid letters. Extra columns and the header row are skipped:

name	sequence	notes
primer_F	ATGGATTTATCTGCTCTTCG	forward
primer_R	CTAAGATTTTCTGCATAGCA	reverse

>primer_F
ATGGATTTATCTGCTCTTCG
>primer_R
CTAAGATTTTCTGCATAGCA

How the converter reads your text

Plain text has no fixed layout, so each line is sorted into sequence, name, or text to skip before any FASTA is written.

• Names: a line such as Human insulin, BRCA1 fragment, seq1:, or Gene: INS names the sequence below it. An identifier followed by a description, such as NM_007294.4 Homo sapiens BRCA1, keeps both in the header. A short all-caps line like GFP counts as a name only when a much longer sequence follows it, and the result tells you when that happened.
• Wrapped sequences: lines under a name are joined into one sequence. Without a name, lines of equal width with a shorter last line (the way databases wrap sequences) are also joined.
• Lists: unnamed lines of different lengths stay separate records, so primer, guide RNA, and peptide lists convert one sequence per line.
• Inline names: seq1: ATGC..., seq1 ATGC..., 1. ATGC..., and two-column name,sequence rows keep the name out of the sequence.
• Existing FASTA: lines that start with > always start a new record and keep their header text. An introduction line or a ; comment before the first header is skipped.
• File formats: GenBank, EMBL, FASTQ, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PDB, and mmCIF input is recognized and converted by its own rules, so a pasted GenBank record gives its accession and definition as the header.
• Document text: invisible characters, soft hyphens, typographic dashes and quotes, and list bullets from Word or PDF copies are cleaned before conversion.

Prose that isn't sequence, such as Here are my sequences:, is skipped and listed in the result. If the layout is ambiguous, Multi-sequences overrides the automatic choice.

Input

Empty files show an error and leave the upload control available. Choose a file containing sequence data to continue without reloading.

Settings

The basic settings cover most inputs. Change Multi-sequences only when the automatic reading of your text is wrong.

The advanced settings control cleanup and validation.

Results

The result opens on the FASTA preview, with a one-line summary above it such as 2 sequences · 101 residues · Protein. When the input came from a recognized format, the summary also says so (read as GenBank).

Changes that could matter show as notices above the preview: removed stop codons or gap characters, letters outside the chosen sequence type, skipped text lines, skipped sequences with the reason, and short lines that were used as names. Removing spaces, numbers, and line breaks is expected and does not raise a notice.

If no sequence passes validation, the result shows the reason and keeps a downloadable run.log in Logs and Files. Correct the input or change the relevant setting to regenerate the preview. A rejected conversion produces no FASTA file.

How to convert a Word document to FASTA

Upload the .docx file directly, or copy the text out of Word and paste it. The document text is extracted in your browser, then read with the same rules as pasted text, so a gene name paragraph above a sequence paragraph becomes one named FASTA record. Formatting such as bold, colors, and tables is ignored; the characters Word inserts invisibly (non-breaking spaces, soft hyphens, curly quotes) are removed. PDF files work the same way when they contain selectable text, not scanned images.

FASTA format rules

FASTA is simple, but a few rules decide whether downstream tools accept a file.

• Header line: each record starts with one line beginning with >. The first word is the identifier and should be unique; anything after the first space is a free-text description.
• Sequence lines: the sequence follows the header. Wrapping at 60 or 80 characters is standard, and one line per sequence is also valid.
• Valid characters: nucleotide codes (A, C, G, T, U, and IUPAC ambiguity codes such as N) or one-letter amino acid codes.
• Alignment gaps: aligned FASTA may contain - or .; turn on Preserve alignment gaps when converting an alignment.
• Stop markers: translated proteins sometimes end in *; turn on Preserve stop codons to keep it. Tools that reject non-letters need it removed, and filtering protein sequences or filtering DNA sequences can clean an existing FASTA file.
• Plain text: no numbering, spaces, or formatting inside sequences, and the file must be saved as plain text.

Which FASTA converter should I use?

TXT to FASTA handles free text in any layout. A more specific converter fits when the input is a structured file or the output isn't FASTA.

The converted file is ready for sequence alignment, BLAST searches, and splitting into smaller FASTA files.

FAQ

How do I convert a text file to FASTA format?

Upload the .txt file or paste its contents, and the converter writes one FASTA record per sequence with a header from the nearest name line. Download the .fasta file or copy the output. Without a converter, add a >name line above each sequence in a text editor and save the file with a .fasta extension.

Can I just rename a .txt file to .fasta?

Only if the file already has a > header line above every sequence. Renaming changes the extension, not the content, so a file of bare sequences stays unreadable to BLAST, aligners, and other FASTA tools.

How do I convert TXT to FASTA with awk?

For lines that hold a name and a sequence, run awk '{ printf ">%s\n%s\n", $1, $2 }' sequences.txt > sequences.fasta. For one unnamed sequence per line, awk '{ printf ">seq_%d\n%s\n", NR, $0 }' numbers the records. Neither joins wrapped lines or removes numbering.

How do I add a header to a sequence in FASTA format?

Put a line that starts with > directly above the sequence. The first word after > is the identifier, for example >INS_human, and anything after the first space is a free-text description.

Can I convert a Word document to FASTA?

Yes. Upload the .docx file or paste its text. The text is extracted in the browser and names above sequences become FASTA headers.

Why did my sequence split into several records?

Unnamed lines of different lengths are treated as a list of separate sequences. Add a name line above the sequence, or choose Join all lines into one sequence under Multi-sequences. The result shows a notice when equal-width lines were split.

How do I create a FASTA file for several sequences?

Paste each sequence under its own name line, or use rows such as name,sequence. Each one becomes a separate record in a single multi-FASTA file.

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 instead of T. Protein uses one-letter amino acid codes plus X, B, Z, J, O, and U.

What happens to duplicate sequence names?

Later duplicates get _2, _3, and so on appended to the identifier, before any description, so every identifier in the file is unique.

How do I convert RNA to DNA in a FASTA file?

Choosing DNA for an RNA sequence skips it rather than deleting its U residues. Convert it with RNA to DNA, which replaces U with T.