New track hubs have been created for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 plant species (read more).
Looking for a plant protein? There is now a new fast protein sequence search in Ensembl Plants, using the Hidden Markov Models (using the search tool HMMER). Just click on the 'HMMER' link in the Ensembl Plants banner (or go directly from here), and add your query sequence in plain text or FASTA format.
Release 31 adds new variation data from Jeffares et al (2015). This covers the 57 strains that were identified to account 99.6% of all SNP in the Schizosaccharomyces pombe genome. It identifies more than 170,000 SNPs and over 14,000 insertion and deletion events.
Some Ensembl Genomes services will be unavailable from approximately 14.00BST on Friday 26th August to 14.00BST on Tuesday 30th August. The main websites will be unaffected but the FTP site and public MySQL server will be unavailable during this time. We apologise for any inconvenience this essential hardware maintenance may cause. E-mails sent to our helpdesk during this time will be held, but no responses sent until Tuesday.
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.
The "virtual" mart names used to identify our live BioMarts will change in release 31 to no longer include the version e.g. protists_mart instead of protists_mart_31. This is to make re-use of URLs etc. easier.
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.
Ensembl Bacteria has been updated to include the latest versions of 39,584 genomes (39,183 bacteria and 401 archaea) from the INSDC archives.
There are legs and tentacles everywhere in this release of Ensembl Metazoa, as ten new species scuttle, swim and slither into our databases. From the tiny Antarctic midge to the charismatic California two-spot octopus, the new species represent the taxonomic diversity of metazoa. There are dog and rat parasites (the itch mite and a nematode), and species that are significant problems for agriculture (Australian sheep blowfly) and aquaculture (the salmon louse and a myxosporean). The common bumblebee is cute and fuzzy (and an important pollinator), a brachiopod represents a new phylum in Ensembl Metazoa, and the African social velvet spider is a fascinating model of sociality, as well as being the first spider genome.
As if all that wasn't enough, we have updated the gene sets for two ants (the leafcutter ant and the red fire ant) and the two-spotted spider mite. The latest gene set updates from VectorBase and WormBase have also been incorporated into this release.
This release of Ensembl Plants includes approximately 350,000 new rice variations across 3,000 rice accessions from 89 different countries as well as track hubs for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 different plant species (read more). More new exciting features are listed here.
Ensembl Protists is now updated to 158 genomes from 104 species containing 1,705,794 protein coding genes. With the addition of Opisthokonts, Monosiga brevicollis genome in pan taxonomic compara (example), we have comparative analysis with protists representatives from all the major Eukaryotic clades.