UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Bioinformatics. 2015 Mar 15;31(6):926-32. doi: 10.1093/bioinformatics/btu739. Epub 2014 Nov 13.


Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters.

Results: Intra-cluster molecular function consistency was examined by analysis of Gene Ontology terms. Results show that UniRef clusters bring together proteins of identical molecular function in more than 97% of the clusters, implying that clusters are useful for annotation and can also be used to detect annotation inconsistencies. To examine coverage in similarity results, BLASTP searches against UniRef50 followed by expansion of the hit lists with cluster members demonstrated advantages compared with searches against UniProtKB sequences; the searches are concise (∼7 times shorter hit list before expansion), faster (∼6 times) and more sensitive in detection of remote similarities (>96% recall at e-value <0.0001). Our results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • AlkB Homolog 5, RNA Demethylase
  • Cluster Analysis
  • Computational Biology*
  • Databases, Protein*
  • Dioxygenases / chemistry
  • Dioxygenases / genetics
  • Dioxygenases / metabolism*
  • Gene Ontology
  • Humans
  • Information Storage and Retrieval
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism*
  • Molecular Sequence Annotation
  • Proteins / chemistry
  • Proteins / genetics
  • Proteins / metabolism*
  • Sequence Analysis, Protein*
  • Software*


  • Membrane Proteins
  • Proteins
  • Dioxygenases
  • ALKBH5 protein, human
  • AlkB Homolog 5, RNA Demethylase