Release 27 adds new wheat variation data from the Hapmap project. The data were generated by re-sequencing 62 diverse wheat lines using whole exome capture and genotyping-by-sequencing (GBS). In total 1.57 million SNPs and 162 thousand small indels were identified across the 21 chromosomes of bread wheat. In addition, the genotypes of 475 individuals have been added to the Axiom 820K SNP Array from CerealsDB.
In collaboration with the Ecole Normale Superieure, Paris and the J. Craig Venter Institute, San Diego, we have re-annotated the genome of the marine diatom Phaeodactylum tricornutum. The new annotation was produced using 13,828 non-redundant ESTs, 42 libraries of RNA-Seq generated using Illumina technology and 49 libraries of RNA-Seq data generated under various iron conditions using SoLiD technology, as well as gene models previously predicted in this and related species. The new gene set contains a total of 12,089 protein coding genes, an increase from the 10,402 genes previously predicted. Models have been checked and corrected through a process of manual curation. The gene models have been analysed using InterProScan and Ensembl Compara and are available to explore in Ensembl Protists.
We're surveying our users to find out more about what you use Ensembl Genomes for, what we do well and what we could do better. The survey should take up only a few minutes of your time, and your answers will be very useful to us: please follow the link to participate https://www.surveymonkey.com/s/HV5T5HZ and feel free to share the link with other users of our service. Thank you!
From release 27 onwards, the Ensembl Genomes BLAST service uses NCBI Blast+ in place of WUBLAST. Please contact us if you have any questions about this change.
Release 28 of Ensembl Genomes is scheduled for 4th August 2015 - more details in Ensembl Genomes Release 28 Intentions. Note that this release is principally concerned with updating to a newer version of the Ensembl platform and contains relatively little additional data.
Hitherto, Ensembl Genomes has made two alternative sequence searches available, one operated by the European Nucleotide Archive (and available through the link 'Sequence Search' in the header of Ensembl Genomes sites), and one using BLAST. The ENA-provided search will be decommissioned for all divisions with the release of Ensembl Genomes 27, currently planned for the end of May. The BLAST service will remain available for all divisions (metazoa, plants, fungi, protists and bacteria).
As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk).
Shortly before the release 27 of Ensembl Genomes in June 2015, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance.
Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps.
The REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval. For more information on these additional endpoints, please visit:
The new server is available at http://rest.ensemblgenomes.org/ - please note that http://beta.ensemblgenomes.org will remain accessible until the next release of Ensembl Genomes in October after which point it will be removed.
The Ensembl Genomes public MySQL server is now located on mysql-eg-publicsql.ebi.ac.uk, port 4157. Please update your scripts to use this new location.
mysql.ebi.ac.uk port 4157 will be retired on 4th December 2014
The 27th release of Ensembl Genomes features updates to version 80 of the Ensembl software across all divisions, including a significant expansion of Ensembl Fungi and Ensembl Protists, bringing the total number of genomes to 23,636 genomes from 4,991 species (full list). Detailed notes can be found here. See the individual homepages for more information.
Ensembl Bacteria has been updated to include the latest versions of 23,000 genomes (22,703 bacteria and 297 archaea from 4,536 species) from the INSDC archives.
Ensembl Fungi has now been expanded to include 355 new genomes representing 236 species, loaded from genome sequence and annotation submitted to INSDC, expanding Ensembl Fungi to 408 genomes from 271 species. A representative selection of these new genomes have been added to the Ensembl Fungi peptide comparative genomics database. Release 27 of Ensembl Fungi also includes an updated release of Schizosaccharomyces pombe.
New wheat variation data from the Hapmap project, re-sequencing 62 diverse wheat lines using exome capture and GBS identifying 1.57 million SNPs and 161,719 small indels. In addition, the genotypes of 475 individuals have been added to the Axiom 820K SNP Array from CerealsDB. The tomato genome and associated genomic data (including variations) have been updated from version 2.40 to version 2.50. As usual, the Assembly converter tool may be used to convert between the coordinates of these two assemblies. Two new array datasets have been added to barley, the Agilent barley full-length cDNA array, and the barley PGRC1 10k A and B array set.
Ensembl Protists has now been expanded to include 101 new genomes representing 66 species, loaded from genome sequence and annotation submitted to INSDC, expanding Ensembl Protists to 133 genomes from 91 species. A representative selection of these new genomes have been added to the Ensembl Protists peptide comparative genomics database.