I know how to generally pull down information for a UniProt entry using the REST API, for example:


I'm looking at this entry as an example. I'm able to pull down most of the attributes I want with a variation of the API query above, however, I'm stuck on one part.

For all human proteins, I want to pull down the peptide sequences that come from that protein.

In the example above, it would be the sequences of the peptides associated with this section:

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Can this be done with the API or do I have to come with a scraping method for all human proteins where I (1) get the protein sequence of each entry, (2) get this table, (3) calculate where the peptides start and end from the sequence in step 1? I feel like this alternative will be much slower, so I want to check I'm not missing anything obvious.

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    $\begingroup$ Downloading the whole of Uniprot and filtering for humans is probably a nicer solution. It is in XML format, which is a bit of a pain, but is a goldmine of data, which you may need —totally depends on your plans and how they may evolve. E.g. I have written my own Python XML Uniprot parser due to my needs and I have a human scraped dataset that is heavily focused on my project which expanded with time. $\endgroup$ Feb 3, 2021 at 12:17

1 Answer 1


If downloading the complete database is not an option, you may able to use the instructions from this help page (based on the gff format for any given query):



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