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Protocols

UniRef specifications

Information


Unique identifier OMICS_03879
Name UniRef
Alternative name UniProt Reference clusters
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainers


  • person_outline UniProt proteomes Team
  • person_outline Baris Suzek

Publication for UniProt Reference clusters

UniRef citations

 (481)
call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] The ISIP1 protein sequence (Phatr3_J55031) was used as the seed sequence for BLASTp analysis against a curated library comprising all protein sequences in UniRef, the MMETSP (), and all additional sequences hosted on the JGI portal. This composite database, described by Dorrell et al. (), is more extensive than any individual resource. Sequences retriev […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
BMC Genomics
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] ed the BLASTp (e-value cutoff of 1e-5) to align the gene models against various proteins databases: non-redundant (NR) database at NCBI, SwissProt-databases containing only manually curated proteins, uniref90 and uniref100-databases containing clustered sets of proteins from UniProt, Pfam-database of protein families and KEGG-database of metabolic pathways. GO analysis of protein sequences were co […]

library_books

Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium

2018
Microbiome
PMCID: 5941691
PMID: 29739445
DOI: 10.1186/s40168-018-0465-9

[…] s, fulfilling either of the above criteria, and this reference was used for further analyses. Functional predictions for this dataset were carried out by BLASTX searching against both the UniProt and UniRef50 databases (UniProt Consortium, 2014). The best hit per transcript with e value < 10−4 was selected, and the description, Gene ontology, KEGG pathway and conserved domain(s) for each hit retri […]

library_books

Transcriptomic analysis of crustacean molting gland (Y organ) regulation via the mTOR signaling pathway

2018
Sci Rep
PMCID: 5943448
PMID: 29743490
DOI: 10.1038/s41598-018-25368-x

[…] For annotation, both nucleotide sequences and predicted peptide sequences were used to run BLAST queries against Swiss-Prot (SP), TrEMBL, and Uniprot Uniref90 protein databases (http://www.uniprot.org/downloads; Fig. ),. SP database was downloaded on September 27, 2016, TrEMBL on October 14, 2016, and Uniref90 on November 28, 2016. Stand-alone soft […]

library_books

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild Type Salmonella enterica Serovar Typhi

2018
MBio
PMCID: 5941076
PMID: 29739901
DOI: 10.1128/mBio.00686-18

[…] ide-level searches were conducted via Bowtie 2 against a functionally annotated pangenome database, ChocoPhlAn, and unmapped reads were searched on a translational level via Diamond (). The resulting UniRef50 gene families were mapped to KEGG Orthogroups (KOs) and Gene Ontology (GO). Differential gene expression analysis was conducted with edgeR to study both global and genus-level gene expression […]

library_books

Diapause in a tropical oil collecting bee: molecular basis unveiled by RNA Seq

2018
BMC Genomics
PMCID: 5923013
PMID: 29703143
DOI: 10.1186/s12864-018-4694-x

[…] Gene annotation was performed by Blastx [] in the Annocript-1.1 software []. The UniRef databases, from September of 2015, were used and results from both UniRef [] and Swiss-Prot [] were considered (p-value 1e-5). In the case of divergence between these two databases, the Swiss-P […]


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UniRef institution(s)
Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, WA, DC, USA
UniRef funding source(s)
Supported by the UniProt grant U01 HG02712 from the National Institutes of Health.

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