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What's New in Release 59

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Ensembl Genomes REST Service

To access Ensembl Genomes data from any programming language, try our REST service. For full documentation, including examples from a wide range of languages, visit http://rest.ensembl.org

In June 2023, Ensembl Bacteria released new gene predictions for almost all of the genomes it hosts. This was done in collaboration with the EMBL-EBI metagenomics team and utlised a pipeline using Prokka, combined with results from cmscan, EggNOG and InterProScan. We have retained the community-submitted annotation for 115 species that are in our pan-taxonomic comparative analysis.

  • Genomes

  • Data

    • New gene predictions for genomes (except for 115 species in pan-taxonomic compara)
    • Updated annotation of molecular interactions involving bacterial genes
    • Alignments to Rfam covariance models (Rfam 12.2) visible in separate track (‘Rfam models’)
    • Updated protein features for all species using InterProScan
    • Updated pan-taxonomic compara (which includes key bacterial species)

Ensembl Rapid Release

New assemblies with gene and protein annotation every two weeks.

Note: species that already exist on this site will continue to be updated with the full range of annotations.

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The Ensembl Rapid Release website provides annotation for recently produced, publicly available vertebrate and non-vertebrate genomes from biodiversity initiatives such as Darwin Tree of Life, the Vertebrate Genomes Project and the Earth BioGenome Project.

Rapid Release news on our blog

Archive sites

The following archive sites are available to access previous versions of data:

Ensembl Bacteria

Ensembl Bacteria is a browser for bacterial and archaeal genomes. The assemblies for these are taken from the databases of the International Nucleotide Sequence Database Collaboration, the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan).

Data access

Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats. A selection of over 100 key bacterial genomes have been included in the pan-taxonomic compara, and genes from all genomes have been classified into families using HAMAP and PANTHER more details.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.

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