Three new variation data sets for Hordeum vulgare (barley) are included in this release. Two are from recent population sequencing (POPSEQ) experiments: ~5 million variant calls from POPSEQ of cv. Morex x cv. Barke progeny, over 6 million variant calls from POPSEQ of Oregon Wolfe barley. In addition, around 7,000 iSelect SNPs, mapped to ~2,600 iSelect markers have been added. These, and all other barley variations, have been accessioned in the transPLANT variation archive. Read more...
Ensembl Plants includes an ordered version of the IWGSC genome assembly for Triticum aestivum (bread wheat). The existing Chromosome Survey Sequence (CSS) contigs were ordered using POPSEQ data from IPK Gatersleben. Additionally, the IWGSC's BAC by BAC assembly and annotation of chromosome 3B replaces the CSS-derived assembly of 3B. Read more...
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.
A training course will be held at the EBI, 1st-3rd July, with a focus on exploring plant variation data. Organised as part of the transPLANT project, the course will contain tutorials and lecutures from staff from many of the leading European institutes working with plant informatics data, including the Ensembl Plants team but also trainers from from the German Research Center for Environmental Health in Munich (the maintainers of PlantsDB), Wageningen University, The Genome Analysis Centre in Norwich, The Gregor Mendel Institute in Vienna, and from two SMEs, Biogemma and Keygene. This exciting course is highly subsidised and we advise early registration. Please click here for more information.
|Our sister project, WormBase-ParaSite, uses Ensembl infrastructure to provide early access to data from pathogenic worms. We are seeking to hire a bioinformatician to work on this project, based at the Wellcome Trust Sanger Institute. Click here for more details.|
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).
Release 27 of Ensembl Genomes is scheduled for 26th May 2015 - more details in Ensembl Genomes Release 27 Intentions.
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
Ensembl Bacteria has been updated to include the latest versions of 21,767 genomes (21,479 bacteria and 289 archaea) from the INSDC archives.
Community-annotated gene names and descriptions have been added for the centipede, Strigamia maritima.
This release of Ensembl Plants includes the latest genome and annotation assembly of Medicago truncatula from the Medicago truncatula Sequencing Consortium (read more). Additionally, seven new whole genome alignments between the Triticeae genomes using the ATAC aligner have been included, including alignments between the Triticum aestivum (bread wheat) component genomes (A, B and D stats), Triticum urartu against the bread wheat A genome (stats), Aegilops tauschii against the bread wheat D genome (stats), Triticum urartu against Aegilops tauschii (stats), and Hordeum vulgare against Triticum aestivum (stats), Triticum urartu (stats) and Aegilops tauschii (stats).
No significant changes have been made to Ensembl Protists for this release.