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What is a UniRef seed sequence compared to a representative sequence?

Last modified June 21, 2019

A UniRef seed is the sequence that has been used as the template to recruit other sequences by the clustering algorithm. The seed sequence is the longest member of a cluster.

However, the longest sequence is not always the most informative one. There is often more biologically relevant information (name, function, cross-references) available on other cluster members. All the proteins in a cluster are therefore ranked as follows to select the most biologically relevant representative sequence for the cluster:

  1. Quality of the entry: manually reviewed entries (i.e. from UniProtKB/Swiss-Prot) are preferred;
  2. Annotation score: entries that have higher UniProtKB annotation scores are preferred. This also means that UniProtKB entries will always take precedence over entries that are in UniParc but not in UniProtKB;
  3. Organism: entries from reference proteomes and model organisms are preferred; and,
  4. Length of the sequence: longest sequence is preferred.


  • The cluster is defined by the identity relationship of its members to the seed, not to the representative sequence. This does not imply that all sequences within a cluster have the same identity percentage among themselves.
  • In some rare cases, a member is more similar to the representative of another cluster than to the representative of its own cluster, but never more similar to any other cluster's seed.
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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