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.

What is new?

  • Molecular and biological information from PHI-base (version 4.0) for thousands of genes in Protists, Bacteria and Fungi that are involved in pathogen-host interactions
  • Small non-coding RNA genes in the diatom Phaeodactylum tricornutum (Rogato et al. 2014)
Phaeodactylumtricornutum_1_1043340_1060257

Small non-coding RNA genes described by Rogato et al (2014) in the diatom P. tricornutum are now available in Ensembl Protists. Hover over the ncRNA genes track (genes coloured in light purple) for more information.

Other news

  • Improved image export functionality from our websites

Check our ‘New image export option in Ensembl‘ post for more details.

Slide1

The images in Ensembl Genomes browser websites can be exported in different formats and resolution. Choose the one that suits you best and click on ‘Download’.

  • Protein domains for Protists, Metazoa, Fungi and Plants recalculated with InterProScan (version 54.0)
  • Updated BioMart: Protists, Metazoa, Fungi and Plants
  • Updated gene trees in Plants

Check out all the changes on our Ensembl Genomes website.

Any questions or comments? Email us.

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.

Image export page

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.

Human_13_32315474_32400266 Human_13_32315474_32400266-2

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.

information iconYou 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.

What’s new in e83:

  • Human: gene set updated to GENCODE 24, and new assembly patches (GRCh38.p5)
  • Manhattan plot track for LD
  • Advanced Filtering and Counts on Variant table
  • Minor allele frequency (MAF) filter on sequence mark-up views

Human gene set update and new assembly patches

chromosome_exceptions

The human gene set now corresponds to GENCODE 24 while the assembly has been updated to include new assembly patches for GRCh38.p5.

Manhattan plot track for linkage disequilibrium

This new linkage disequilibrium (LD) track is focused on a variant and displays the linked variants surrounding the focus variant. The track displays a Manhattan plot, using the r2 and D prime values (from 0 to 1) on the Y axis. The new track is accessible in the Variation Linkage disequilibrium page, through the links in the new column “LD Manhattan plot“.

Manhattan_plot_track_LD

Advanced Filtering and Counts on Variant table

The functionality of the variant table has been further expanded to allow a wider range of filtering options. Filtering can now be applied by Minor Allele Frequency, SIFT and PolyPhen scores, Clinical Significance, Consequence Type and many other columns, using buttons along the top of the variant table. For many of these filters, preset useful combinations of options are available within the popup allowing rapid configuration of more complex combinations. In addition, row counts for each consequence type have been readded to the existing Consequence Type filter. These are displayed in the popup which appears once the filter button has been pressed.

Filtering variants in RYR1 gene (ENSG00000196218).

MAF filter on sequence mark-up views

The variants displayed on all sequence mark-up views can be filtered by minor allele frequency (MAF), allowing you to either show or hide according to a range of frequencies (between 0.01% and 10%). This filtering is not on by default so to enable it go to ‘Configure this page’ on any sequence view page and then choose the value you want from the ‘Hide variants by frequency (MAF)’ drop down menu.

Consequence filter for MAF.Improving the image export and Ensembl mobile website

There are many updates to these functionalities which will be described in detail in separate blog posts. Look out for these blogs! Below is how the new image export wizard looks like.

Image export window

Other news

  • Mouse: updated to GENCODE M8 annotation
  • Rat: updated gene set, including manually annotated HAVANA annotation
  • Annotations now available in RDF format for all species on our FTP site
  • New human phenotype association data from Cancer Gene Census
  • RefSeq genomic to mRNA comparison attributes will be updated for human
  • New dbSNP145 variation data for chicken and pig

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 December, 4pm GMT. Register here.

Ensembl 83 is scheduled for December 2015 and includes:

Updated gene sets and annotations

  • Human: gene set updated to GENCODE 24, and new assembly patches (GRCh38.p5)
  • Mouse: updated to GENCODE M8 annotation
  • Rat: updated gene set, including manually annotated HAVANA annotation

Variation data imports and updates

  • Phenotype data updated for several species including human, mouse, rat, horse and turkey
  • New human phenotype association data from Cancer Gene Census
  • New and updated studies from DGVa for several species such as human, mouse, macaque, cow and dog
  • Latest sequence variants from dbSNP build 145 for chicken and pig
  • New “ExAC” evidence, variation set and track
  • dbSNP rsIDs now available for gibbon

Other highlights and data sets

  • RefSeq genomic to mRNA comparison attributes will be updated for human
  • Improved image export
  • GFF3 support for userdata
  • Annotations in RDF format for all species

 

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.

What is new?

  • Pairwise alignments for more than 50 plant genomes including potato and tomato, cacao and grape, and several Oryza sp
  • Newly available genomes from INSDC into our ever expanding Protists and Fungi divisions
  • Cross-references of genes in Fungi and Protists to the Pathogen – Host Interaction Database (PHI-base)
  • Additional 6,806 bacterial genomes imported from ENA
  • Protein domain information from InterProScan (version 5.14-53.0)

Genomic alignments

New pairwise alignments have been extended to additional plant genomes and can be viewed in our browser website. The alignment text can be downloaded in different file formats.

Comparing the genomic region of the Patatin gene in two plant species, potato and tomato.

Comparing the genomic region of the Patatin gene in two plant species, potato and tomato.

In addition to the graphical view, whole genome alignments can be retrieved via our FTP or programmatically using our APIs.

View the complete list of genomic alignments available in this new release.

Marking your favourite region, gene, exon, or variant

You can now mark a selected region when browsing the Ensembl Genomes websites. Drag and select your favourite gene and use the pop-up window to mark it. You can also click on the gene itself to mark the location of it.

Slide1

Highlighting a genomic region in Ensembl Genomes is now available in many of our views.

Other news

  • Updated BioMart: Protists, Metazoa, Fungi and Plants
  • Updated peptide comparative genomics
  • New assemblies and annotations for existing fungal species
  • Gene families available in Protists

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

Any questions or comments? Get in touch.

The second update of the GRCh37 archive site has now been released. Some of the data imports and updates for this release include:

  • dbSNP144 human data including data from the Exome Aggregation Consortium (ExAC)
  • Public HGMD data (version 2015.2)
  • Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet and Decipher
  • Exome Sequencing Project data (v.0.0.30. (Nov. 3, 2014))
  • HumanCoreExome-12 chip
  • Gene annotation dumps in GFF3 format

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.

What’s new in e82:

Ensembl mobile website

We are very happy to announce the release of the Ensembl website mobile version, available on http://m.ensembl.org. This new website allows you to quickly search for a gene, variants or phenotype on your mobile device.

Ensembl mobile website

Support of VEP Plugins through the web interface, script and REST

The VEP can now be extended beyond its core functionality using a system of plugins. Plugins are a powerful way to extend, filter and manipulate the output of the VEP. More information regarding the VEP plugins can be found on the following documentation page.

Improved Variation tables

Variation tables for genes and transcripts have been reimplemented to effectively handle the large number of variants now known for many genes. At the same time, the ability to filter, sort, and select this data has been improved. Filtering by variant type is now achieved by selecting the “Type:” filter at the top of the main table. Further features and refinements are expected to be added in forthcoming releases.

new_Variation_table

Zebrafish development stage RNASeq data set

We’ve added sample-specific BAM files, splice junctions (introns) and gene models based on a range of zebrafish developmental stages and tissue samples.

Zebrafish_BAM_track

Marking a region on images

A new feature to mark a selected region has been added to the location, gene and other views. Marking can be applied by drag-selecting a region and then using the zmenu to mark it, or by clicking on a feature on an image and then using the zmenu to mark the location of the feature.

LastZ replaced TBlat for pairwise alignments

We have replaced TBlat with LastZ and recomputed 9 pairwise alignments using LastZ. TBlat was used for distantly related species as it was yielding a higher genome coverage, but over time we have optimised the LastZ parameters that enable it to give a 50-100% increase in genome coverage.

Other news

  • Human variation data updates to dbSNP (144) including variants from the Exome Aggregation Consortium (ExAC)
  • Mouse: updated to GENCODE M7 including HAVANA annotation.
  • Improved data upload form
  • Improvements to PDF export
  • Export mode for projectors and print
  • Phenotype data updated for several species, including human, mouse, rat and horse

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 7th October, 4pm BST. Register for free.

Ensembl 82 is scheduled for September 2015 and includes:

Updated gene sets and annotations

  • Human variation data updates to dbSNP (144) including variants from the Exome Aggregation Consortium (ExAC)
  • Mouse: updated to GENCODE M7 annotation
  • Zebrafish: RNASeq data from developmental stages

Other highlights and data sets

  • Extra functionality for the VEP web and REST interfaces (via plugins)
  • Phenotype data updated for several species, including human, mouse, rat and horse
  • HGMD (version 2015.2), and NHLBI Exome Sequencing Project data, HumanCoreExome-12 chip variants
  • Improved data upload web form

Second update to the GRCh37 site

This release will also see a fresh update to our dedicated GRCh37 site (grch37.ensembl.org) with:

  • Variant data from dbSNP144 which includes variants from the Exome Aggregation Consortium (ExAC)
  • Updated variants from NHLBI Exome Sequencing Project and HGMD (2015.2)
  • Phenotype data from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Orphanet and Decipher
  • Variants from the HumanCoreExome-12 chip

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.

What is new?

pomGO

Gene Ontology (GO) annotations are some of the updates for S. pombe genes in Ensembl Fungi release 28

Slide1

Protein domains updated from InterProScan for Fungi, Protists, Metazoa and Plants in this new release

  • Updated BioMart: Protists, Metazoa, Fungi and Plants.

Any questions or comments? Get in touch.