Paste your text
Nothing pasted yet — everything is processed locally in this tab.
Conversion options
FASTA output
Your FASTA output will appear here as you paste and configure on the left.
How to convert text to FASTA
- 1
Paste your sequence text
Copy the raw sequence text from your document, terminal or notes and paste it into the input box. A single sequence, one sequence per line, or sequences separated by blank lines all work.
- 2
Choose how records are split and name them
Pick the split mode that matches your text (one record, one per line, or blank-line blocks), then set the sequence ID prefix and optional description that become the > header line.
- 3
Check the preview and statistics
The converter reports the record count, total residues, sequence type (DNA/RNA or protein) and GC content, and warns about duplicate headers or invalid characters before you export.
- 4
Copy or download the FASTA file
Press Copy to place the formatted FASTA on your clipboard, or Download .fasta to save it as a file ready for NCBI BLAST, EMBL-EBI tools, samtools, seqtk, GenBank submission or your pipeline.
About the Text to FASTA Converter
The Text to FASTA Converter turns pasted plain text into a valid FASTA file in your browser: paste the sequence, set the header, and copy or download the result. The whole format is just a header line beginning with > that names the sequence, followed by the sequence itself — this tool generates both correctly every time.
Real sequence data rarely arrives as clean FASTA. It is copied out of a spreadsheet with cell numbers, out of a PDF with line breaks every 70 characters, out of a report with spaces between codons, or as raw bases from a sequencing provider with no header at all. The converter strips the noise, applies the wrapping you choose, and builds unique > headers so the output opens directly in NCBI BLAST, EMBL-EBI Clustal Omega, MEGA, EMBOSS, samtools, seqtk, IGV or any pipeline that reads FASTA.
It handles one sequence or hundreds: split the pasted text into one record per line, one record per blank-line separated block, or keep everything as a single record, and each record gets a numbered ID such as sample_1, sample_2, sample_3. Everything runs in the page — no upload, no account, no file size limit beyond your own browser memory.
What this tool does
Three ways to split records
Treat the whole paste as one sequence, one sequence per line, or one record per blank-line block. That covers a single read, a plate of sequences pasted from a spreadsheet, or a multi-record file without any manual editing.
Proper > headers you control
Set an ID prefix and description that become the header line, with automatic _1, _2 numbering for multiple records. Existing lines that already start with > can be preserved as-is, so half-formatted input does not lose its annotations.
Automatic sequence cleanup
Spaces, tabs, line breaks, digits from numbered copies and stray punctuation are removed from the sequence body, because none of them are valid FASTA characters. A counter reports exactly how many characters were stripped.
Line wrapping at 60, 70 or 80
Sequence lines are wrapped at a fixed width — 60 characters is the convention used by NCBI, 70 is the classic FASTA width — or left as one continuous line, which some simple parsers prefer.
Validation before you export
The output panel reports record count, total residues, length range, GC percentage for nucleotide input, and detects whether the text is DNA/RNA or protein, warning you about duplicate headers and unusual characters.
Copy, download, stay private
Copy the result to the clipboard or download a .fasta file. The conversion is plain string processing in your browser tab, so unpublished constructs, clinical samples and proprietary sequences never leave the machine.
Example commands
# input (one sequence per line)
ATGCATGCATGCATGC
GGTTCCAAGGTTCCAA
# output
>sequence_1
ATGCATGCATGCATGC
>sequence_2
GGTTCCAAGGTTCCAASplit mode: one record per line. Two lines of text become two FASTA records with unique auto-generated IDs.
# input (paste from a numbered document)
1 atg cgt acg tta gcc
2 agg atc cta ggc att
# output
>insert_1 PCR product
ATGCGTACGTTAGCCAGGATCCTAGGCATTDigits and spaces stripped, sequence uppercased, custom ID and description applied, wrapped at 60 characters.
# input (already has headers)
>NC_000913.3 Escherichia coli K-12
ATGAAACCGGCCACTG
CCGCCTGCTGCTGCTG
# output (header preserved)
>NC_000913.3 Escherichia coli K-12
ATGAAACCGGCCACTGCCGCCTGCTGCTGCTGKeep lines starting with > enabled: existing headers and annotations survive, only the sequence body is cleaned and rewrapped.
# multi-record statistics
Records : 96
Residues : 115,200
Type : DNA/RNA
GC : 51.4%A full 96-well plate of sequences pasted at once is parsed, validated and summarised before export.
Frequently asked questions
What is a FASTA file?
A FASTA file is a plain text file that stores one or more biological sequences, where each record starts with a header line beginning with the greater-than sign (>), such as >my_gene description, followed by the sequence characters on the lines below. The format was introduced with the FASTA software package by David Lipman and William Pearson in 1985 and remains the universal interchange format for sequences: NCBI GenBank, EMBL-EBI, UniProt, BLAST, samtools, seqtk, IGV and virtually every bioinformatics pipeline read it. There are no column headers, delimiters or quality strings — just the > header and the sequence, which is why converting plain text into this shape is all this tool does.
How do I convert plain text to FASTA?
Paste the text into the input box, choose how it should split into records, set the sequence ID, and copy or download the output. Concretely: paste your raw bases, select one record for a single sequence, one record per line for a list of sequences, or one record per block when sequences are separated by blank lines; type an ID prefix such as sample so headers become sample_1, sample_2; then press Copy or Download .fasta. The preview updates as you type, so you can check the record count, total residues and GC percentage before exporting.
Can I convert multiple sequences at once?
Yes. Paste all of them and use one record per line if every sequence is on its own line, or one record per block if they are separated by blank lines. Each record receives a numbered header derived from your ID prefix (sample_1, sample_2, and so on), and the summary table lists every header with its length so you can spot an empty or truncated record before downloading. Hundreds of sequences paste comfortably in one go; the only limit is browser memory, which is effectively far above what most text-based sequence lists reach.
What line length should FASTA sequences use?
Wrapping sequence lines at 60 or 70 characters is the standard convention: 60 is what NCBI writes for deposited records, and 70 is the classic FASTA width used by many older tools. The format itself does not forbid long lines — most parsers accept a sequence on a single unwrapped line — but wrapping keeps large files diffable, greppable and openable in editors without horizontal scrolling. Choose 60 for maximum compatibility with NCBI-style pipelines, 70 for traditional FASTA, or no wrapping if a downstream script expects one continuous line per record.
What characters are allowed in a FASTA sequence and header?
A nucleotide sequence may contain A, C, G, T, U and the IUPAC ambiguity codes (N, R, Y, S, W, K, M, B, D, H, V); a protein sequence uses the one-letter amino acid codes plus B, Z, X, J, U and O. Spaces, digits, line breaks and punctuation are not valid inside the sequence body, so this converter strips them and reports how many were removed. In the header, everything after the > is free text: the first word is the sequence ID and the rest is a description. Keep the ID unique and free of spaces, and use the description for annotations such as strain, gene or experiment.
Does converting text to FASTA change my sequence?
No. The converter only reformats: it removes characters that are never valid in a FASTA sequence body (spaces, tabs, line breaks, digits and punctuation), optionally changes letter case, and inserts line breaks at the width you choose. No bases are substituted, reversed, complemented or trimmed — the residue count shown in the statistics is the number of sequence characters left after cleaning. If you need to change the sequence itself, such as reverse complementing or subsequence extraction, use the FASTA/FASTQ Tools page after converting.
Is my sequence data uploaded to a server?
No. The conversion is ordinary string processing that runs inside your browser tab; the text you paste is never transmitted or stored. That matters for the sequences people most often convert — unpublished constructs, patient-derived samples, proprietary strains and embargoed results. You can verify it yourself: the page makes no network requests with your data, and the copy and download operations read directly from browser memory. The same privacy statement applies to every tool on this site and is described in the privacy policy.
What can I do with the FASTA file afterwards?
Anything that reads FASTA: run a similarity search with NCBI BLAST or EMBL-EBI FASTA, align sequences with Clustal Omega, MAFFT or MEGA, inspect them in IGV or UCSC Genome Browser, manipulate them with seqtk and samtools, submit them to GenBank or ENA, or feed them into your own pipeline. It is also the format expected by the other tools on this site — the Sequence File Converter, FASTA/FASTQ Tools and Sequence Aligner all take the output of this converter directly.
Related tools
All processing happens locally in your browser. Nothing you upload is transmitted or stored, as described in the privacy policy.