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Forthcoming changes

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Browser support change: End of support for Microsoft Internet Explorer

On February 24, 2021

We will phase out support for Microsoft's Internet Explorer (IE 11), since our user base for this web browser is continuously decreasing and has significantly fallen below 1.5%. Please switch to a more recent and supported browser in order to enjoy the full functionalities of the UniProt website.

Even if you are not using IE 11, it may be a good idea to look at the list of the browsers we support and consider switching to the most recent version of your browser for the best user experience and security.

Changes to the FTP repository for reference proteomes

On February 24, 2021

We currently distribute the UniProt reference proteomes on our FTP site in four taxonomic division folders (Archaea, Bacteria, Eukaryota and Viruses) and provide for each proteome its sequences in FASTA format and mappings from UniProt identifiers and gene names to those found in other databases. Starting from the next release, we will also publish the full protein records for a proteome in the UniProtKB text and XML format, and we will at the same time introduce a subfolder for each proteome that groups all its files in order to reduce the number of files in the taxonomic division folders.

Example: UP000005640

Current FTP folder and files:

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/

  • UP000005640_9606.fasta.gz
  • UP000005640_9606_additional.fasta.gz
  • UP000005640_9606_DNA.fasta.gz
  • UP000005640_9606_DNA.miss.gz
  • UP000005640_9606.idmapping.gz
  • UP000005640_9606.gene2acc.gz

New FTP folder and files:

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/

  • UP000005640_9606.dat.gzUniProtKB text format
  • UP000005640_9606.xml.gzUniProtKB XML format
  • UP000005640_9606.fasta.gz
  • UP000005640_9606_additional.fasta.gz
  • UP000005640_9606_DNA.fasta.gz
  • UP000005640_9606_DNA.miss.gz
  • UP000005640_9606.idmapping.gz
  • UP000005640_9606.gene2acc.gz

Changes to the humsavar.txt file and related keywords

On February 24, 2021

The humsavar.txt file lists all missense variants annotated in UniProtKB/Swiss-Prot human entries. It provides a variant classification which is intended for research purposes only, not for clinical and diagnostic use. Variants are currently classified into the categories Disease, Polymorphisms and Unclassified. We will rename these categories to follow the terminology recommended by the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) (Richards et al. PubMed:25741868):

Old category New category Description
Disease LP/P likely pathogenic or pathogenic
Polymorphism LB/B likely benign or benign
Unclassified US uncertain significance

Current format:

Main      Swiss-Prot             AA             Type of
gene name AC         FTId        change         variant       dbSNP          Disease name
_________ __________ ___________ ______________ _____________ ______________ _____________________
...
CC2D2A    Q9P2K1     VAR_075698  p.Trp1182Arg   Disease       rs386833755    Joubert syndrome 9 (JBTS9) [MIM:612285]
CC2D2A    Q9P2K1     VAR_076881  p.Ser117Arg    Unclassified  rs186264635    Joubert syndrome 9 (JBTS9) [MIM:612285]
CC2D2A    Q9P2K1     VAR_076882  p.Lys507Glu    Polymorphism  rs144439937    Joubert syndrome 9 (JBTS9) [MIM:612285]
...

New format:

Main      Swiss-Prot             AA             Variant
gene name AC         FTId        change         category dbSNP          Disease name
_________ __________ ___________ ______________ ________ ______________ _____________________
...
CC2D2A    Q9P2K1     VAR_075698  p.Trp1182Arg   LP/P     rs386833755    Joubert syndrome 9 (JBTS9) [MIM:612285]
CC2D2A    Q9P2K1     VAR_076881  p.Ser117Arg    US       rs186264635    Joubert syndrome 9 (JBTS9) [MIM:612285]
CC2D2A    Q9P2K1     VAR_076882  p.Lys507Glu    LB/B     rs144439937    Joubert syndrome 9 (JBTS9) [MIM:612285]
...

Also in line with the ACMG/AMP guidelines, we will at the same time deprecate the keyword "Polymorphism" and rename the keyword "Disease mutation" to "Disease variant", because the terms 'polymorphism' and 'mutation', which have been used widely, often lead to confusion due to incorrect assumptions of pathogenic and benign effects, respectively.

Entries with variant annotations can be retrieved on the UniProt website with the query annotation:(type:variant).