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What is a redundant proteome? Can reference proteomes become redundant? Can reviewed UniProtKB (Swiss-Prot) entries be deleted when a proteome becomes redundant?

Last modified May 29, 2015

What is a redundant proteome?

A redundant proteome is one in which all or nearly all protein sequences are highly similar or identical to an existing proteome from the same species.

To reduce redundancy in proteomes and subsequently UniProtKB/TrEMBL, we have developed a procedure to identify highly redundant proteomes within species groups, using a combination of manual and automatic methods.

  • Proteomes can only be redundant to other proteomes of the same taxonomy branch at species level or below (sub-species, strains, etc.).
  • We use the CD-Hit 2D program for pairwise comparison of proteomes within each taxonomic group. Based on the results, we calculate the level of similarity between pairs of proteomes within the groups.
  • Proteomes that rank lowest are the most redundant. These are marked as “redundant” on the UniProt proteomes portal (example: UP000008521, redundant to UP000008520), and are labelled with a specific icon . Protein entries belonging to these redundant proteomes are either removed from UniProtKB/TrEMBL, or, for new sequences, no corresponding UniProtKB/TrEMBL entries are created. The sequences from redundant proteomes are available for download from the UniProt sequence archive UniParc via the proteomes portal.

See also:
Reducing proteome redundancy
Elimination of redundant proteomes (UniProt Blog)

Can a reference proteome be made redundant?

No, reference proteomes have a special status that protects them from becoming redundant. Reference proteomes are carefully chosen based on stringent criteria and represent important organisms covering the tree of life with a high level of annotation.

Can reviewed UniProtKB (Swiss-Prot) entries be deleted when a proteome becomes redundant?

No. While it can happen that a proteome containing reviewed UniProtKB (Swiss-Prot) entries becomes redundant, its reviewed, manually curated members are not deleted as a consequence.