2
$\begingroup$

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

https://www.uniprot.org/uniprot/?query=id:Q9UJL9&sort=score&columns=id,go(molecular%20function)&format=tab

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:

enter image description here

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.

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ 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. $\endgroup$
    – Matteo Ferla
    Commented Feb 3, 2021 at 12:17

1 Answer 1

Reset to default
1
$\begingroup$

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):

https://www.uniprot.org/help/download_subsequences

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.