Evidence map›Paper›PMID 25398609›Full record

ArticleBioinformatics (Oxford, England)2015

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

Baris E Suzek, Yuqi Wang, Hongzhan Huang, Peter B McGarvey, Cathy H Wu, UniProt Consortium

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In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,052 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,052citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1,052 citing papers in PubMed, 1 synthesis or guideline pooled it.

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  19. HFGuidedDesign:Chemical science · 2026
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992 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Baris E SuzekProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
Yuqi WangProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
Hongzhan HuangProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
Peter B McGarveyProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
Cathy H WuProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
UniProt Consortium

Funding

UniProt: A Centralized Protein Sequence and Function ResourceU41HG006104 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI APWEILER, ROLF · 2010 to 2014
$23.5M
UniProt: A centralized protein sequence and function resourceU41HG007822 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI BATEMAN, ALEX · 2014 to 2017
$21.9M
NHGRI NIH HHS U41HG006104NHGRI NIH HHS U41 HG007822
6 · The paper itself

Abstract

motivationUniRef 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.

resultsIntra-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.

Indexed as

Computational BiologyDatabases, ProteinSequence Analysis, ProteinSoftwareAlkB Homolog 5, RNA DemethylaseCluster AnalysisDioxygenasesGene OntologyHumansInformation Storage and RetrievalMembrane ProteinsMolecular Sequence AnnotationProteinsALKBH5 protein, humanAlkB Homolog 5, RNA DemethylaseDioxygenasesMembrane ProteinsProteins

Identifiers

PMID25398609
PMCPMC4375400

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.