Ensembl BlogEnsembl 91 is now live! The cat is truly out of the bag now, and we can safely say that there’s been no monkeying around this release; we’ve been very busy!
Read on to discover the highlights of this new release and be sure to join us for our release webinar at 16:00 (GMT) on Wednesday 13th December for a guided tour of the new data and site.
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Ensembl 83 is scheduled for December 2015 and includes:
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
The second update of the GRCh37 archive site has now been released. Some of the data imports and updates for this release include:
We have re-built the GRCh37 dedicated Ensembl, Regulation and Variation BioMarts to integrate the updated data sets.
You will find a complete list of the changes on the Ensembl GRCh37 website.
Ensembl 82 is scheduled for September 2015 and includes:
This release will also see a fresh update to our dedicated GRCh37 site (grch37.ensembl.org) with:
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
Ensembl 81 is scheduled for July 2015. Highlights include:
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
Annotation of the recent human assembly, GRCh38, was released in e76 in August 2014. Since then we have been maintaining a dedicated site to the GRCh37 assembly. The reason for updating annotations on the previous human assembly is to support those users who may still have data annotated on the old assembly, and who can not yet run their analyses on the new assembly. The Genome Reference Consortium (GRC) keeps a blog on the assemblies that they maintain which may be a good source of information if you are still contemplating a move to GRCh38. If you are wondering about the migration from GRCh37 to GRCh38 within Ensembl, we published a blog series which may be of interest.
We are now pleased to announce that the GRCh37 archive site has been updated with new human data sets. In addition to data imports, we have also utilised the improved regulatory build pipeline for mapping all available human regulatory features to the GRCh37 assembly. We have also re-built the GRCh37 Ensembl, Regulation and Variation BioMarts to integrate the updated data sets.
Highlights from some of the data imports for this release are:
A complete list of the changes can be found on the Ensembl GRCh37 website.
The human gene set now corresponds to GENCODE 22 while the assembly has been updated to include new assembly patches for GRCh38.p2.
The HG-126 patch (KN538364.1) in GRCh38.p2 corrects a misassembly in this region which affects the RYBP gene.
In this release we provide comparisons between the imported RefSeq transcripts in human to all overlapping Ensembl models. The comparison is done at the transcript level where all exons are compared in terms of genomic coordinates and the transcript sequences of the two models are also compared. Additionally, we have also compared the genomic sequences of the RefSeq transcripts to the Ensembl models. Both of these data sets are available via our API.
It is now possible to view the Gene gain/loss tree with our new interactive view (which uses the same engine as the species tree view introduced last release). Click on the toolbar to change the layout of the tree or on a node to get its details and expand, collapse, or focus on it.
Our REST server now implements the Global Alliance for Genomics and Health (GA4GH) Genomics API. The aim of the GA4GH API is to allow the interoperable exchange of genomic information across multiple organisations and on multiple platforms – see http://ga4gh.org/#/api for further details. Phase 3 genotype data from the 1000 Genomes project is now available from Ensembl via three new GA4GH endpoints.
Genotype data for three sheep species have been imported from the NextGen project. The project aims to preserve the biodiversity of farm animals. The imported populations are Iranian Ovis aries and Ovis orientalis and Moroccan Ovis aries. You can read more about other NextGen data set on the Ensembl projects.
A complete list of the changes can be found on the Ensembl website.
Find out more at the Ensembl Release Webinar e79 (16.00 GMT, Thursday 26th March). Register here (for free!).
It is now possible to get instant VEP results for single variant queries; simply paste a variant in any format into the box and click the button. For more detailed results you can still submit the request in the usual manner.
The mouse genome assembly has been updated to include new assembly patches for GRCm38.p3. We are now displaying GENCODE M4 in Ensembl.
This new assembly patch, KB469738.2 (MG132_PATCH), provides a fix for chromosome 9 for genes Nlrp4g and Ppp2r3d.
We have updated the APPRIS flags for human and mouse and also imported the data for rat and zebrafish. APPRIS, a system for annotating principal coding isoforms, is a joint project between Centro Nacional de Investigaciones Oncologicas and Instituto Nacional de Bioinformatica. These are now available in BioMart.
The human and mouse genome assemblies comprise haplotypes (eg. MHC, LRC) and other alternate sequences where the same gene may be annotated in more than one of the alternate sequences. The gene summary page has now been improved to display all manually annotated alternative alleles for a gene. This is available from the left-hand side menu under ‘Gene alleles’.
Alternate alleles for GNL1 (ENSG00000206412) can be compared by clicking the Region Comparison link.
It is now possible to view the Ensembl species tree with our new interactive view. Once on the Species tree page, click the link “View the full Ensembl species tree”. You can select between Ensembl and NCBI taxonomy trees, and choose to view only a subset of species at a time.
Export options for the comparative genomics views have undergone major changes in recent releases and in e78 we have finalised this work. The GeneTrees can now be exported in multiple formats. This option is available dirctly by the GeneTree image, replacing the ‘Gene tree (text)’ and ‘Gene tree (alignment)’ options. Orthologues and paralogues can be downloaded only in OrthXML format while gene gain/loss trees can be downloaded in PhyloXML format.
Available options for exporting GeneTrees.
A complete list of the changes can be found on the Ensembl website.
Find out more at the Ensembl Release Webinar e78 (Wednesday, 17 Dec 4-4:30 GMT). Register here (for free!): http://tinyurl.com/e78-webinar.
Ensembl 78 is scheduled for December 2014. Highlights include:
Alternate alleles for GNL1 (ENSG00000206412) can be compared by clicking the Region Comparison link.
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.
Ensembl 77 is scheduled for release in October 2014. Highlights for the coming release include:
For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.