FASTA to CSV converter
Paste or upload FASTA and download a CSV or TSV table for spreadsheets, or a plain text file with one sequence per line.
Input
How to convert FASTA to CSV?
Paste FASTA records or upload a .fasta file, and the FASTA to CSV converter writes one table row per sequence with id, description, length, and sequence columns. Wrapped sequence lines are joined into a single cell. Choose TSV for tab-separated output or TXT for sequences only, then download the file or copy it.
Two UniProt entries, converted with the default settings:
>sp|P01308|INS_HUMAN Insulin OS=Homo sapiens OX=9606 GN=INS PE=1 SV=1
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPL
ALEGSLQKRGIVEQCCTSICSLYQLENYCN
>sp|P01344|IGF2_HUMAN Insulin-like growth factor 2 OS=Homo sapiens OX=9606 GN=IGF2 PE=1 SV=1
MGIPMGKSMLVLLTFLAFASCCIAAYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLE
TYCATPAKSERDVSTPPTVLPDNFPRYPVGKFFQYDTWKQSTQRLRRGLPALLRARRGHVLAKELEAFREAKRHRPLIALP
TQDPAHGGAPPEMASNRKid,description,length,sequence
sp|P01308|INS_HUMAN,Insulin OS=Homo sapiens OX=9606 GN=INS PE=1 SV=1,110,MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
sp|P01344|IGF2_HUMAN,Insulin-like growth factor 2 OS=Homo sapiens OX=9606 GN=IGF2 PE=1 SV=1,180,MGIPMGKSMLVLLTFLAFASCCIAAYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYCATPAKSERDVSTPPTVLPDNFPRYPVGKFFQYDTWKQSTQRLRRGLPALLRARRGHVLAKELEAFREAKRHRPLIALPTQDPAHGGAPPEMASNRKThe identifier is everything before the first space in the header, and the description is the rest. A description containing a comma or quote is wrapped in quotes so spreadsheet programs keep it in one cell:
>primer_F forward, exon 2
ATGGATTTATCTGCTCTTCG
>primer_R reverse
CTAAGATTTTCTGCATAGCAid,description,length,sequence
primer_F,"forward, exon 2",20,ATGGATTTATCTGCTCTTCG
primer_R,reverse,20,CTAAGATTTTCTGCATAGCAHow to convert FASTA to TXT
Set Output format to TXT (one sequence per line). Headers are dropped and each sequence is written on its own line, ready for tools or scripts that expect bare sequences:
ATGGATTTATCTGCTCTTCG
CTAAGATTTTCTGCATAGCATo keep names alongside the sequences in a text file, use TSV (tab-separated) instead. The same primers as TSV:
id description length sequence
primer_F forward, exon 2 20 ATGGATTTATCTGCTCTTCG
primer_R reverse 20 CTAAGATTTTCTGCATAGCAOpen the result in Excel or Google Sheets
Download the .csv file and open it, or copy the preview and paste it into a sheet. TSV pastes into separate columns directly in both programs. Very long sequences fit in a cell: Excel holds up to 32,767 characters per cell, which covers most proteins and genes, while whole chromosomes and genomes are better kept in FASTA.
Input
| Input | Description |
|---|---|
FASTA input | Pasted FASTA or one uploaded .fasta, .fa, .faa, .fna, .ffn, .fas, .mfa, or .txt file up to 50 MB. Lines starting with ; are skipped as comments. Records with a header but no sequence are skipped and reported. |
Text without any > header is not FASTA; convert it with TXT to FASTA first.
Settings
| Setting | Description |
|---|---|
Output format | CSV (comma-separated) (default), TSV (tab-separated), or TXT (one sequence per line). |
Separate ID and description | CSV and TSV only. On (default), the header is split into id and description columns. Off, the whole header goes into one header column. |
Include length column | CSV and TSV only. Adds a length column with the number of characters in each sequence. Default: on. |
Include column names | CSV and TSV only. Starts the file with a row of column names. Default: on. |
Sequence case | Keep original (default), Uppercase, or lowercase. |
Sequences are copied as they are, apart from joining wrapped lines and removing whitespace. Gaps, stop markers, and ambiguity codes stay in the output, so the length column counts them too.
Results
| Tab | Contents |
|---|---|
Preview | The converted file as text, with a summary such as 2 sequences · CSV file. |
Files | The .csv, .tsv, or .txt file, named after the uploaded file or sequences for pasted input. |
Table | Every record as a table (up to the first 5,000 records). |
Which tool should I use?
| Goal | Tool |
|---|---|
| FASTA to a spreadsheet or plain sequence list | FASTA to CSV |
| A spreadsheet back to FASTA | CSV to FASTA |
| Plain text or a Word file to FASTA | TXT to FASTA |
| GenBank, FASTQ, or an alignment to FASTA | FASTA converter |
| One FASTA file into many smaller files | FASTA splitter |
FAQ
How do I convert a FASTA file to Excel?
Convert it to CSV, download the .csv file, and open it in Excel. Each sequence becomes a row with its identifier, description, length, and sequence.
How do I get only the sequences from a FASTA file?
Choose TXT (one sequence per line). Headers are removed and each sequence is written on one line.
Does the converter change my sequences?
No. Wrapped lines are joined and whitespace is removed; letters, gaps, and stop markers stay as they are unless you change Sequence case.
Can I convert the CSV back to FASTA?
Yes, with CSV to FASTA, which reads the id and sequence columns this tool writes.
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