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How to retrieve sets of protein sequences?

Last modified June 2, 2017

UniProtKB entries are available in three file formats – Flat Text, XML and RDF/XML. UniProtKB entries in these formats each contain only one protein sequence, the so-called ‘canonical’ sequence. UniProtKB canonical sequences are also available in FASTA format, as are additional manually curated isoform sequences that are described in UniProtKB/Swiss-Prot. Below we describe how these sets can be accessed.

In addition to the predefined FASTA, XML, RDF/XML and text formats, search results can also be downloaded in tab-separated or Excel format, reflecting your own customizable column settings.

See also:

What is the canonical sequence? Are all isoforms described in one entry?

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Retrieving sequences from the website

  • Perform your favorite query and view the resulting list of entries (e.g. this query retrieves all UniProtKB entries that are part of the human proteome: proteome:UP000005640)
  • Click the Download button in the query result page
  • Choose the desired download format (Flat Text, XML, RDF/XML, tab-delimited, Excel or FASTA if additional isoform sequences are desired)
    • Choosing Flat Text, XML, or RDF/XML allows retrieval of all entries (and their canonical sequences) from the result list in the desired format.
    • Choosing FASTA (canonical) format allows retrieval of all canonical sequences from the query result list. This can include canonical sequences from both UniProtKB/Swiss-Prot and/or UniProtKB/TrEMBL entries.
    • Choosing the option FASTA (canonical and isoform) allows retrieval of all canonical sequences plus all manually reviewed isoform sequences described within UniProtKB/Swiss-Prot. These manually reviewed isoform sequences are available as distinct sequences in FASTA format only within this expanded downloadable set.
    • Choosing Tab-separated or Excel allows retrieval of your search result table reflecting the columns you have chosen to include.

To automate the above, please read the section Downloading data at every UniProt release of our Programmatic access documentation.

Retrieving sequences from the FTP site

The UniProt FTP sites (accessible via the Download latest release link located on the home page) provide the most frequently requested data sets in each of the aforementioned file formats (Flat Text, XML, RDF/XML, FASTA). The additional manually curated isoform sequences that are described in UniProtKB/Swiss-Prot are available in a separate FASTA file (uniprot_sprot_varsplic.fasta.gz). Our FTP directory also includes expanded FASTA sets, containing both the canonical and manually reviewed isoform sequences, for all reference proteomes.