We will make changes to the directory layouts of both the Ensembl Genomes FTP server (ftp://ftp.ensemblgenomes.org/pub/) and the Ensembl GRCh37 FTP server (ftp://ftp.ensemblorg.ebi.ac.uk/pub/grch37/) that may affect your pipelines. These changes will come into effect in Ensembl Genomes release 43/Ensembl release 96, which are scheduled for April 2019. Here are the details, so that you can plan any required updates to existing scripts and pipelines ahead of the releases.
If you’ve been at VizBi 2019, you’ll have seen Andy Yates previewing our new website design. If not, here’s your chance to take a look.
As of Ensembl release 96/Ensembl Genomes release 43, we will retire rest.ensemblgenomes.org and invite you to use rest.ensembl.org instead.
In the next release of Ensembl (Ensembl 96) we will remove our database patches script from the main Ensembl repository.
There is now a dedicated module using the EBI OLS service to load Ensembl required ontologies. Considering this module is now in charge of loading the required data, the previous databases patches have been moved to the ols-ensembl-loader repository.
If you need to update your system with future patches, please now refer to the ols-ensembl-loader repository sql directory where files are already available.
Please contact the Ensembl Helpdesk if you have any questions or want to find out more about how this might affect your work.
We are planning to release Ensembl 96 and Ensembl Genomes 43 in late March or beginning of April 2019.
The Ensembl 96 release includes the first pass full annotation of the mouse genome, with the GENCODE M21 gene set.
The Ensembl Genomes 43 release will bring changes to our REST API and FTP server that may affect your pipelines. Specifically, we will merge our Ensembl and Ensembl Genomes REST servers into a single server. We will also change the Ensembl Genomes Comparative Genomics FTP file structure to make it consistent with Ensembl.
We have got lots of new genomes: 19 birds, five reptiles and 12 mammals, which include primates, rodents, American mink, American bison and wild yak.
We also have an exciting first release of Ensembl-RefSeq MANE Select v0.5 transcripts!
The archive website for Ensembl release 74 will be retired. This is inline with our rolling retirement policy, where archives are retired after five years, unless they contain the last instance of an important dataset for a key species.
We’ve just released Ensembl Genomes 42, with new and updated plant species, including soya and tomato, as well as three new species for Ensembl Metazoa.
The latest version of Ensembl, release 95, is out. This release brings a brand new human regulatory build for GRCh37 and GRCh38, incorporating new data from the ENCODE and Roadmap epigenomics project, plus an update to the mouse GENCODE gene set. We’ve also got a whole host of new vertebrate species, updated genome assemblies for some important agricultural species and the brand new protein structure viewer.
We’re planning to release the next versions of Ensembl and Ensembl Genomes in December.
We’ve got some exciting new genomes, including polar bear, as well as updated genome assemblies for three important agricultural species. We’ve also got a new regulatory build for the human GRCh38 and GRCh37 assemblies and a brand new protein structure variation view.
In its latest release, Ensembl has completely reviewed its reporting of potential Transcription Factor (TF) binding sites. TF proteins are key players of gene expression regulation that bind to specific DNA regions characterised by approximate sequence patterns, or transcription factor binding motifs (TFBM). These motifs are generally represented as a Position Specific Frequency Matrix, or Binding Matrix. Ensembl scans genomes for occurrences of these motifs, reporting Motif Features at each possible location.