UniProt Protein Scraper
Pricing
from $7.50 / 1,000 results
UniProt Protein Scraper
Scrapes UniProt protein entries from a search query and returns each one as a flat row with accession, protein name, gene, organism, function, and sequence. No API key required.
Pricing
from $7.50 / 1,000 results
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ParseForge
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UniProt Protein Scraper
Scrape UniProt protein entries by name, gene, or accession, up to a million per run. Every entry returns its accession, protein name, gene, organism, function, and sequence. No API key or registration. Export to JSON, CSV, Excel, or XML.
UniProt's public API requires you to paginate, map fields, and handle rate limits for every query. This Actor reads the UniProt knowledge base directly from a single search term, collects each matching protein entry, and returns them in one flat, consistent schema. It works for Swiss-Prot reviewed entries and TrEMBL unreviewed entries alike.
| Who uses it | What they scrape UniProt for |
|---|---|
| Bioinformaticians | Fetching protein sequences and functional annotations for a gene family in one batch. |
| Drug discovery researchers | Pulling target protein metadata and sequences to feed docking or screening pipelines. |
| Academic labs | Building a local dataset of reviewed Swiss-Prot entries for a specific organism. |
| Data journalists | Collecting protein function descriptions and organism data for a story on a biological pathway. |
What it does
This Actor collects UniProt protein entries from a search query and returns each one as a flat row with accession, protein name, gene, organism, function, and sequence.
- ๐ฌ Protein-centric search: query by protein name, gene symbol, or UniProt accession, and get the full entry back.
- ๐ Flat row output: every protein is one row with accession, protein name, gene, organism, function, and sequence, ready for analysis.
- โ๏ธ Configurable volume: set a maximum from 1 to 1,000,000 proteins per run to control scope and runtime.
- ๐พ Multi-format export: download your dataset as JSON, CSV, Excel, or XML with one click.
Results export to CSV, JSON, Excel, or XML, or straight from the API.
What you can do with UniProt data
๐งฌ Fetch a gene family's sequences.
A bioinformatician queries a gene name, sets maxItems to 500, and downloads all matching protein sequences and functional annotations for a multiple sequence alignment.
๐ Build a target list for docking.
A drug discovery researcher searches an organism and a functional keyword, collects the top 2000 entries, and exports them to CSV for a virtual screening pipeline.
๐ Create a reviewed-protein dataset.
An academic lab queries a model organism, limits to 10,000 proteins, and filters the output to Swiss-Prot entries for a course dataset.
๐ฐ Gather function descriptions for a story.
A data journalist searches a pathway name, pulls 100 entries, and uses the function field and organism data to fact-check a piece on a biological mechanism.
Why choose this scraper
| What you get | |
|---|---|
| No API key | Reads the public UniProt knowledge base directly, no registration or token management. |
| Fixed schema | Every row has the same fields: accession, protein name, gene, organism, function, and sequence. |
| Reviewed and unreviewed | Collects both Swiss-Prot and TrEMBL entries in the same run. |
| Scale on demand | From a single protein to a million, the Actor scales to your query without changing the setup. |
How it compares
This Actor focuses on a flat, consistent row per protein with the full sequence included, while the other UniProt scrapers on Apify offer different field sets or pricing models.
| Feature | ParseForge | UniProt Protein Scraper - Sequences, Genes & Function | UniProt Proteins Scraper - Protein Metadata | Uniprot Scraper |
|---|---|---|---|---|
| Full amino acid sequence | Yes | Yes | Not listed | Not listed |
| Protein function description | Yes | Yes | Not listed | Not listed |
| Gene name | Yes | Yes | Yes | Not listed |
| Organism | Yes | Yes | Yes | Not listed |
| No per-result cost | Yes | Not listed | Yes | Yes |
| Configurable max items per run | Yes | Not listed | Not listed | Not listed |
Configure the run
Drive the Actor from a single UniProt search query, and set a maximum item count so only the first N matches reach your dataset. The Input tab lists every parameter.
A first run with the defaults:
A larger pull:
Pricing
Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.
| Results collected | Approximate cost |
|---|---|
| 100 results | $0.85 |
| 1,000 results | $8.50 |
| 10,000 results | $85.00 |
New Apify accounts start with $5 in free credit.
Free users
Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.
Run it
- Create a free Apify account with $5 in credit.
- Open the UniProt Protein Scraper.
- Set your inputs and any filters, then click Start.
- Export the results as CSV, Excel, JSON, or XML from the Dataset tab.
Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.
Use with AI agents (MCP)
Give an AI agent live access to UniProt through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:
Then prompt it in plain language to run the scraper and read back the results.
Troubleshooting
Why am I getting no results?
Check that your query matches entries in UniProt. Try the same search term on the UniProt website first. Also verify that maxItems is set to a number greater than 0.
Why is the run taking so long?
Large maxItems values mean the Actor must fetch many pages. Reduce maxItems to a smaller number, or narrow your query to a more specific protein name or organism.
Why are some fields empty in my output?
Not every UniProt entry has a gene name or a curated function description. Empty fields mean UniProt does not hold that data for the entry, not that the Actor missed it.
Why did I get fewer results than maxItems?
The Actor stops when the query has no more matches. If your search term returns only 42 proteins, setting maxItems to 100 will still give you 42 rows.
Can I filter by reviewed status during the run?
The Actor does not filter by reviewed status while scraping. Collect the full result set and then filter your dataset for Swiss-Prot entries by their accession prefix or the reviewed field after the run.
FAQ
| Question | Answer |
|---|---|
| Do I need a UniProt API key? | No. This Actor reads the public UniProt knowledge base directly, so you do not need to register an application or manage a key. |
| What fields does each row contain? | Every row returns the UniProt accession, protein name, gene name, organism, function description, and the full amino acid sequence. The exact field list is shown in the sample output on the Actor's page. |
| Can I get only Swiss-Prot reviewed entries? | The Actor collects both Swiss-Prot and TrEMBL entries. You can filter the output dataset after the run by the reviewed flag or accession prefix. |
| How many proteins can I scrape in one run? | You set the maximum in the input, from 1 up to 1,000,000 proteins. The Actor stops when it reaches that count or when the query has no more matches. |
| What search terms can I use? | You can search by protein name, gene symbol, or UniProt accession. The query is passed directly to UniProt's search, so any term that works on the UniProt website will work here. |
| Does it return the protein sequence? | Yes. The full amino acid sequence is included in every row. |
| Can I search by organism? | Yes. Include the organism name in your query, for example 'human albumin' or 'E. coli lacZ', and the Actor will return matching entries. |
| What output formats are supported? | You can export your dataset as JSON, CSV, Excel, or XML from the Apify platform. |
| Is this faster than the UniProt API? | It avoids the per-request rate limits and pagination code you would write against the REST API. For large queries, it can collect thousands of entries in a single run without manual looping. |
| Can I run this on a schedule? | Yes. You can set up a recurring schedule on Apify to re-run the Actor daily or weekly and keep your protein dataset up to date. |
Related actors
Browse the full ParseForge collection for more scrapers.
๐ Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.
โ ๏ธ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by UniProt Consortium. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.
