Answers.Body: <p>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):</p>
  <p><a href="https://www.uniprot.org/help/download_subsequences" rel="nofollow noreferrer">https://www.uniprot.org/help/download_subsequences</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-08T08:36:09.570Z
Answers.LastActivityDate: 2021-03-08T08:36:09.570Z
Answers.UserDisplayName: Elisabeth.Gasteiger
Body: <p>I know how to generally pull down information for a UniProt entry using the REST API, for example:</p>
  <p><a href="https://www.uniprot.org/uniprot/?query=id:Q9UJL9&amp;sort=score&amp;columns=id,go(molecular%20function)&amp;format=tab" rel="nofollow noreferrer">https://www.uniprot.org/uniprot/?query=id:Q9UJL9&amp;sort=score&amp;columns=id,go(molecular%20function)&amp;format=tab</a></p>
  <p>I'm looking at <a href="https://www.uniprot.org/uniprot/Q9UBU3" rel="nofollow noreferrer">this</a> 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.</p>
  <p>For all human proteins, I want to pull down the peptide sequences that come from that protein.</p>
  <p>In the example above, it would be the sequences of the peptides associated with this section:</p>
  <p><a href="https://i.sstatic.net/HcDzq.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/HcDzq.png" alt="enter image description here" /></a></p>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-03T12:17:46.270Z
Comments.Text: 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](https://github.com/matteoferla/MichelaNGLo-protein-module/blob/master/michelanglo_protein/generate/_protein_uniprot_mixin.py) due to my needs and I have [a human scraped dataset](https://github.com/matteoferla/MichelaNGLo-human-protein-data) that is heavily focused on my project which expanded with time.
Comments.UserDisplayName: Matteo Ferla
Tags: <uniprot><api>
Title: How to extract all peptide sequences for a UniProt protein entry with an API?
ThreadText: # How to extract all peptide sequences for a UniProt protein entry with an API?
  
  (Asked by: username_0 on 2021-01-29)
  
  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](https://www.uniprot.org/uniprot/Q9UBU3) 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](https://i.sstatic.net/HcDzq.png)](https://i.sstatic.net/HcDzq.png)
  
  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.
  
  **Tags:** uniprot, api
  
  > **Comments:**
  > **username_1**: 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](https://github.com/username_1/MichelaNGLo-protein-module/blob/master/michelanglo_protein/generate/_protein_uniprot_mixin.py) due to my needs and I have [a human scraped dataset](https://github.com/username_1/MichelaNGLo-human-protein-data) that is heavily focused on my project which expanded with time.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-03-08. Score: 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):
  
  <https://www.uniprot.org/help/download_subsequences>
  
  
  ---
  
  