This bumper release of Ensembl Plants brings eight new genomes, including cassava, cotton, cucumber, green bean, sunflower and yam. In addition we have updated to latest and greatly improved (v3.0) sorghum genome assembly from JGI as well as updated assemblies for both soybean and peach. Users can now view, query, download and analyse our comparative analysis of nearly 2 million genes across 53 plant species.

All 12 drosophilid species in Ensembl Metazoa have been updated with data from FlyBase, including a gene set update for Drosophila melanogaster (dmel_r6.17) and a new assembly for Drosophila simulans (dsim_r2.02).

Advanced Course on Fungal Pathogen Genomics

A Wellcome Trust Advanced Course on Fungal Pathogen Genomics will take place from 13th-18th May 2018, Hinxton, Cambridge. This course provides hands-on training on how to take advantage of unique tools offered by a number of leading fungal databases, including Ensemb Fungi, to develop testable hypotheses, and interrogate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces. Daily activities at the workshop will include individual and group hands-on training exercises, supplementary lectures on bioinformatic techniques and tools used by various databases, and presentations by distinguished guest speakers. Follow the link to learn more and apply for your place!

posted 2018-01-04
Ensembl Genomes Archive Sites Now Available

Ensembl Genomes now has archive sites for all divisions. These can be found at the following URLs:

http://oct2017-metazoa.ensembl.org

http://oct2017-plants.ensembl.org

http://oct2017-fungi.ensembl.org

http://oct2017-protists.ensembl.org

http://oct2017-bacteria.ensembl.org

The archive sites will allow researchers to access data from old releases via our web-based tools, and additionally will be able to display track hubs containing alignments and features located on older versions of genome assemblies that have since been upgraded in the live site. Archive sites will be searchable and BioMarts will be available where they were produced for the site when live. Schema and API versions for archive sites will be the same as when the data was released, i.e. archive sites will not be updated to use the most recent versions. Ensembl tools will not be active in the initial release, but we are hoping to enable these shortly; likewise, archival REST servers will not initially be available, but will be added in future. Major bugs (i.e. those impeding the usability of the site) will be fixed, but minor bugs will not be.

The first release of the archive sites contains content from release 37. New archive sites will be released at least once a year, under URLs indicating the date of first release of the data they contain. The previously existing archive for Ensembl Plants, http://archive.plants.ensembl.org, will continue to be available at this URL, but also as http://mar2016-plants.ensembl.org, in accordance with the new naming scheme. As previously, data from all recent releases will continue to be available for download at ftp://ftp.ensemblgenomes.org.

posted 2017-11-07

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

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Frequently Asked Questions (FAQs) are now available for all domains of Ensembl Genomes. Have a question? Check if it's been asked before! If there is a FAQ missing, contact us.

What's New in Release 38 (January 2018)

No significant updates have been made for this release.

Release 38 includes a new set of external references to the Rhea database, an expert curated resource of biochemical reactions for the annotation of enzymes. There has also been a new run of Interproscan across all the fungal peptides, and updated biomarts. There have been no significant updates to the genomes.

Ensembl Metazoa welcomes one new species this release, the charmingly-named buff-tailed bumblebee, an important pollinator in Europe. There are updates for the 28 species that we share with FlyBase, VectorBase, and WormBase, including the new gene sets for Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans, plus new assemblies for Brugia malayi, Drosophila simulans and Rhodnius prolixus. There is also a new assembly and gene set for the monarch butterfly.

Pairwise whole genome alignments are now available between Drosophila melanogaster and every dipteran in Ensembl Metazoa, and also for all pairs of hymenopteran species. These alignments are combined with other sources of data to provide metrics that underlie the assertion of a "high confidence" set of orthologues.

This bumper release of Ensembl Plants brings eight new genomes, including cassava, cotton, cucumber, green bean, sunflower and yam. In addition we have updated to latest and greatly improved (v3.0) sorghum genome assembly from JGI as well as updated assemblies for both soybean and peach. Users can now view, query, download and analyse our comparative analysis of nearly 2 million genes across 53 plant species.

Release 38 includes a new set of external references to the Rhea database, an expert curated resource of biochemical reactions for the annotation of enzymes. There has also been a new run of Interproscan across all the protist peptides, and updated biomarts. There have been no significant updates to the genomes.

Release notes from previous releases