What’s new in Ensembl Genomes 31?

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 Antarctic midge to the California two-spot octopus, the new species illustrate the diversity of metazoa. Our new Metazoan species also include dog and rat parasites (the itch mite and a nematode), as well as species that pose significant problems for agriculture (Australian sheep blowfly) and aquaculture (the salmon louse and a myxosporean). The common bumblebee is an important pollinator, a brachiopod represents a new phylum in Ensembl Metazoa, while the African social velvet spider is a fascinating model of sociality and is the first spider in Ensembl Genomes.

Not to be outdone, Ensembl Protists is now updated to 158 genomes from 104 species and Ensembl Bacteria has been updated to include the latest versions of 39,584 genomes (39,183 bacteria and 401 archaea) from the INSDC archives.

Other news

Check out all the changes on our Ensembl Genomes website.

Any questions or comments? Email us.

What’s new in e84:

• Human: Incorporation of BLUEPRINT Epigenome data and methylation data
• Pairwise Linkage Disequilibrium (LD) calculation on LD variant page
• Track hub registry interface
• Transcript haplotype view

Incorporation of BLUEPRINT Epigenome data

BLUEPRINT is a large scale research project aimed at deciphering the epigenome of blood cells. ChIP-seq and DNase hypersensitivity data from the BLUEPRINT project has now been incorporated into Ensembl. All of the cell types analysed in the BLUEPRINT project are listed here. In Ensembl 84, we are including BLUEPRINT data for the following 20 independent cell types, divided based on cell lineage and tissue source:

CD14+ CD16- monocyte from Venous Blood
CD14+ CD16- monocyte from Cord Blood
CD4+ ab T cell from Venous Blood
CD8+ ab T cell from Cord Blood
CM CD4+ ab T cell from Venous Blood
eosinophil from Venous Blood
EPC from Venous Blood
erythroblast from Cord Blood
HUVEC prol from Cord Blood
M0 macrophage from Cord Blood
M0 macrophage from Venous Blood
M1 macrophage from Cord Blood
M1 macrophage from Venous Blood
M2 macrophage from Cord Blood
M2 macrophage from Venous Blood
MSC from Venous Blood
naive B cell from Venous Blood
neutro myelocyte from Bone Marrow
neutrophil from Cord Blood
neutrophil from Venous Blood

This data can be viewed alongside other tracks in Ensembl by using the ‘Configure this Page’ option and selecting your cells of interest.  

Pairwise LD calculation

You are now able to calculate linkage disequilibrium (LD) between any two variants in Ensembl. To calculate the r2 and D’ values for LD between two specific variants, enter the ID of any variant into the LD calculation text box on the specific page of the reference variant. This feature can be found by clicking on ‘Linkage Disequilibrium’ from the menu on any variant page.

Track Hub registry interface

With the arrival of the new Track Hub Registry, we have added a feature that allows you to search for track hubs of interest and attach them directly to Ensembl. Just click on the ‘Add your data/Manage your data’ button on any Ensembl page, and select ‘Track Hub Registry Search’ from the lefthand menu. 

The interface will only search for hubs that have assemblies available for the site you are on; to see the full range of species and assemblies, visit the Track Hub Registry site directly.

Transcript haplotype view

The transcript haplotype view is a new data view we have implemented that allows you to explore observed transcript sequences that results from variants identified from resequencing data from the 1000 Genomes Project. By clicking on the ‘Haplotypes’ link on any transcript page, you are able to view protein consequences, population frequencies and protein alignments of all the haplotypes for that particular transcript.

Other news

• Mouse: update to GENCODE M9 annotation
• Zebrafish: updated gene set, including manually annotated HAVANA annotation
• Baboon: lincRNA model update
• Latest sequence variants from dbSNP build 146 for human, cow and dog
• Import of COSMIC 75 cancer data
• New and updated studies from DGVa for several species such as human, mouse, zebrafish, macaque, cow and dog
• Gene trees: new option to prune by target species/ taxon in the REST API
• Ensembl Families now defined by an HMM library, based upon the Panther database.
• Alignments in CRAM format
• DAS support ended
• Regulatory segments retired from the Ensembl regulation BioMart, but now available in bigbed format through the ftp site

A complete list of the changes can be found on the Ensembl website.

Find out more about the new release, and ask the team questions, in our free webinar. Wednesday 16th March, 4pm GMT. Register here.

Ensembl 84 is scheduled for March 2016 and includes:

Updated gene sets and annotations

• Human: Incorporation of Blueprint epigenome data and methylation data
• Mouse: update to GENCODE M9 annotation
• Zebrafish: updated gene set, including manually annotated HAVANA annotation and RNAseq data update
• Cow: ncRNA data update and transcriptomic data update
• Baboon: lincRNA model update

Variation data imports and updates

• Phenotype data updated for several species including human, mouse, rat, zebrafish and pig
• Latest sequence variants from dbSNP build 146 for human, cow and dog
• HGMD data update
• Import of COSMIC 75 cancer data
• New and updated studies from DGVa for several species such as human, mouse, zebrafish, macaque, cow and dog

Other highlights and data sets

• Pairwise LD calculation on LD variant page
• Alignments in CRAM format
• Track hub registry interface
• Gene trees: new option to prune by target species/ taxon
• DAS support ended
• Regulatory segments retired from the Ensembl regulation Biomart, but now available in bigbed format through the ftp site

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.

Would you like to include images from Ensembl during a presentation or in your paper or poster?

We are happy to announce that a new image export option is available in Ensembl 83, which optimises colour and contrast settings for presentation on a projector or in print. You can download images from Ensembl using the ‘Export this Image’ icon, at the top-left of every image. Below is the image download form, showing the new export options.

Presentation options
Our new export feature for presentations alters the image to be clearly visible on projectors by:

• saturating colours to improve contrast in brightly lit environments
• increasing line breadth for viewing from a distance.

You can see the difference below. On the left is a ‘Standard Web’ exported image. On the right is the same exported image with the ‘Presentation’ feature.

Print options
If you’re looking for an image for your paper or poster, try our new print options, labelled ‘Journal/report’ and ‘Poster’. Images exported for print have a high resolution, which produce x2 and x5 enlargements respectively.

Other export options
You can also export the standard web image in PNG or PDF format for use on the web, or SVG format by clicking on the ‘Custom image’ export option.

You can find more information about exporting images by clicking on the information icons in the export menu.

We would love to hear from you if you have used the new image export options for your own work. Image parameters can be tweaked, so we welcome feedback on whether these features suit your needs. Leave your comments below or contact the Ensembl helpdesk.