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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.

Notes:

  • 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.
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