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Ensembl Genomes specifications


Unique identifier OMICS_01648
Name Ensembl Genomes
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Ensembl_genome_database_project


  • person_outline Paul Kersey

Publication for Ensembl Genomes

Ensembl Genomes citations


Waggawagga CLI: A command line tool for predicting stable single α helices (SAH domains), and the SAH domain distribution across eukaryotes

PLoS One
PMCID: 5812594
PMID: 29444145
DOI: 10.1371/journal.pone.0191924

[…] ts such as protein sequence datasets generated by whole-genome annotations, we selected protein annotation datasets from species across the eukaryotic tree of life (). The datasets were obtained from Ensembl Genomes release 87 []. The overall runtime per dataset ranged from a few hours to seven days depending on dataset size. The average runtime for single sequences ranged from 4.6 to 23.3 seconds […]


Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

PLoS Biol
PMCID: 5747502
PMID: 29253856
DOI: 10.1371/journal.pbio.2004086

[…] initially found to be ‘missing’ in either one, two, or three of the 10 species analysed in this study. For this subset of genes, we searched for the presence of an as-yet-unannotated ortholog in the Ensembl genomes using blastn. In cases where a clear ortholog was detected, we included this gene within the appropriate orthogroup. In total, we identified an additional 18 genes that were added to t […]


De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data

Mol Biol Evol
PMCID: 5850335
PMID: 29216381
DOI: 10.1093/molbev/msx311

[…] gp in genes or ORFs in the high-quality G. morhua and M. aeglefinus genomes, or in the other codfish draft genomes, even with an E-value of 0.1. Furthermore, BLAST got no hits to afgp in Uniprot, the Ensembl genomes or Genbank (except other afgp sequences). De novo genes are more likely to arise in GC-rich genomic regions as these regions are more transcriptionally active and these areas are more […]


Expression Atlas: gene and protein expression across multiple studies and organisms

Nucleic Acids Res
PMCID: 5753389
PMID: 29165655
DOI: 10.1093/nar/gkx1158

[…] Baseline expression data from Expression Atlas continue to be automatically included in Ensembl, Ensembl Genomes, Gramene (), Ensembl Plants (), Reactome () and Plant Reactome (), via Javascript-based widgets. Since the last update, the baseline expression widget is also available through WormBas […]


Gene3D: Extensive prediction of globular domains in proteins

Nucleic Acids Res
PMCID: 5753370
PMID: 29112716
DOI: 10.1093/nar/gkx1069

[…] r 59 000).Despite the more conservative approach in building the HMMs, Gene3D v16 has improved sequence coverage of domain assignments compared to v14. Mapping between releases, using a shared set of Ensembl genomes sequences and scaling to the equivalent search space (based on the -Z hmmsearch parameter set to 10 000 000 and an independent e-value cut-off of 0.001, which we now apply as our defau […]


Ensembl Genomes 2018: an integrated omics infrastructure for non vertebrate species

Nucleic Acids Res
PMCID: 5753204
PMID: 29092050
DOI: 10.1093/nar/gkx1011

[…] Ensembl Genomes (http://www.ensemblgenomes.org) is organised as five sites, each focused on one of the traditional kingdoms of life: bacteria, protists, fungi, plants and (invertebrate) metazoa. Verte […]


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Ensembl Genomes institution(s)
The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; USDA-ARS, Cornell University, Ithaca, NY, USA

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