The VEP can work as an offline or a web tool and it’s also available as REST service. Perfect for integrating into pipelines or displaying data on the web, the REST API VEP endpoints can take input as HGVS, genomic loci or variant identifiers and can interpret common forms of non-standard HGVS. They are all available using both GET and POST protocols, supporting queries on single or multiple variants respectively.
Ever come across a transcript that seems to span multiple genes? These are called ‘readthrough transcripts’, or sometimes ‘conjoined genes’, and they’re more common than you might think. Read on to find out about what they are and what they do, and how we annotate these at Ensembl.
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!
Due to a major loss of cooling incident at one of the EMBL-EBI data centres, there was reduced Ensembl functionality between Saturday 2nd February and Wednesday 6th February.
However, as of Wednesday 6th February, all Ensembl and Ensembl Genomes services have now been restored and are working as normal.
If you encounter any further issues, please report them to the Ensembl Helpdesk.
Thank you for your understanding and patience while we worked to fully restore our services.
Identifying the causal variants from a GWAS generally involves identifying the haplotype blocks that contain your variant of interest, rather than the variant and the gene it is affecting itself. To find the actual genes involved, you need to consider all variants in LD with your identified associations. Ensembl Post-GWAS analysis pipeline (PostGAP) can provide automatic fine-tuning of your GWAS variants, incorporating regulatory information and population-wide LD calculations, along with your VEP results.
A brand new regulatory build for the human GRCh38 and GRCh37 assemblies was released in Ensembl 95 earlier this week. The new regulatory build incorporates data for 55 new and 38 updated epigenomes from the ENCODE project. So what are the differences from the previous regulatory build?
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.