Batch FASTA Processor — One Tool or a Chained Pipeline
Apply one operation — or a chain of them — to every record in a multi-FASTA and export a single CSV/TSV table.
Run the same analysis over a whole multi-FASTA file in one pass — the batch step that is painful to do by hand or in a chat. Paste a multi-FASTA (or one sequence per line) and pick any batchable SeqBench tool — reverse complement, translate, GC content, length, ORFs, primer melting temperature, oligo analysis, restriction sites, protein properties, CAI, characterize and more — and get one tidy table with a name column plus the tool's result columns for every record. The same batch run is callable programmatically via POST /api/v1/batch. Preview it on the page and download it as CSV or TSV for Excel, R or pandas.
0 records detected
Runs … over every record on the server.
Loading tools…
Paste a multi-FASTA (or one sequence per line) or drop a folder's worth of FASTA / GenBank / SnapGene .dna files, pick a tool and run it over every record to build a downloadable table. Records that arrive with features keep them, and go back out as annotated GenBank. Every batchable SeqBench tool is available here, and the same job can be run programmatically via POST /api/v1/batch.
Need more than one step? Chain them
The table above runs ONE tool over every record. A pipeline runs several, each step taking the sequence the previous one produced — reverse complement, then translate, then protein properties — over the whole file in a single pass, with a per-record trace of what each step did.
Paste or drop records above, and the pipeline runs over every one of them.
The same pipeline runs programmatically via POST /api/v1/workflow.
How to use the Batch Processor tool
- 1Paste a multi-FASTA file, or one sequence per line (load the example to see the format).
- 2Pick which SeqBench tool to run over every record, and choose CSV or TSV output.
- 3Read the results table on the page, then copy it or download the CSV/TSV.
Frequently asked questions
What input formats does the batch processor accept?
A multi-FASTA file (each record starts with a '>' header line) or plain sequences with one per line. FASTA headers become the row names; when there are no headers, records are auto-named seq_1, seq_2 and so on.
Which operations can I run over every sequence?
Any batchable SeqBench tool, including reverse complement, translate, GC content, length, ORFs, primer melting temperature, oligo analysis, restriction sites, protein properties, CAI and characterize — not a fixed list. Each record is run through the tool you pick and its result columns are added to the table.
Can I download the results as a table?
Yes. The result is a single table with a name column plus the tool's result columns; you can preview it on the page, copy it, or download it as a CSV or TSV file to open in Excel, R or pandas.
Can I run this from code?
Yes — the same batch run is callable programmatically via POST /api/v1/batch, and every underlying tool is also available over the REST API and the MCP server. You can also share a link that reproduces the exact input and operation.
More
Guides
Related tools
Paste any unknown sequence and get a full identity report, then send it to BLAST.
Paste a sequence and find out what it is, against the whole of GenBank, with the program chosen for you.
Find CpG islands by either published definition, with the observed/expected CpG ratio reported separately from GC content.