What’s new in e!75?

• New VEP interface
• New “Age of base” track for human
• A link to individual exons is now available in the Region in Detail page
• New Gencode Basic Gene Set renderer for human and mouse

New VEP interface

Ensembl has a number of data tools that can benefit from offline processing to overcome the time-out limits imposed by the web. We have therefore created a new interface where you can submit data to these tools and view all your tickets: the first to be ported is the VEP, with others planned for future releases.

The new VEP interface will allow you to process many more variants and is shipped with a new job page where you can easily monitor all your recent tickets, edit, remove or save them into your account. More details on the input form and job page can be found on the VEP Input page.

The result page has been greatly improved, various statistics are now listed in a table
including lines of input read, variants processed and variants remaining after filtering. The result page also includes pie charts showing detailed proportions of consequence types called across all variants. The page now allows you to export the result table in VCF, VEP and TXT format. More details about the results can be found on the VEP Results page.

New “Age of base” track for human

We have added a new track for human, showing the timing of the most recent mutations as determined by inter-species whole genome alignments. You can find the track in the comparative genomics menu under “Conservation regions” (or search for “age of base”).

Each base pair in which the human reference genome differs by substitution from one of its inferred ancestral genomes is coloured in either grey (event prior to the primate branch), blue (primate specific), red (human-specific, fixed variant), or yellow (human-specific segregating variant, i.e. SNP). Clicking on a mutation position reveals the sub-tree of species which have inherited the same mutation from their common ancestor. It also reveals a score that represents the age of the mutation in arbitrary units, and determines the intensity of the colouring. The more recent the mutation, the lower the score and the darker the colour.

Note that this is a beta version of the track – if you find it useful, please let us know!

Individual exon link in the Region in Detail

The popup menu that appears when you click on a transcript now includes a link to the Exon table. The Exon ID from this popup will be displayed in bold on the Exon page.

Note that this link will only appear when you are zoomed in enough for the click coordinates to clearly identify a single exon.

GENCODE Basic Gene Set Renderer

You can now view the GENCODE gene set in a new way, called “GENCODE Basic”. The new GENCODE Basic display option shows only a only a subset of the GENCODE transcripts.

When using the GENCODE Basic display option, partial transcripts will not be shown if the gene includes complete (Met to Stop) transcripts. Problematic biotypes (eg. retained intron) are excluded from the basic set.

The full GENCODE gene set will be available as before, using the standard display options such as “Expanded with labels”.

Other news:

• Updated zebrafish gene set to include manual annotation from Havana
• Added RNA-seq data for mouse
• Added variation data for turkey from dbSNP build 139
• Imported the latest sequence variants from dbSNP build 139 for dog, horse, opossum, platypus and zebra finch.
• Imported mouse phenotype data from IMPC (International Mouse Phenotyping Consortium)
• Updated variation citations from EPMC and UCSC
• Highlighting of the current feature can now be disabled
• Updated Caenorhabditis elegans reference annotation to Wormbase WS240
• Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1 and liftover mapping added

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

Find out more at the Ensembl Release Webinar e75 (Wed, Mar 12, 2014 4:00 PM – 4:20 PM GMT). Register for free here: http://tinyurl.com/e75webinar

Ensembl 75 is scheduled for release in February 2014. Highlights for the coming release include:

New web features

• New integrated Tools interface for BLAST and VEP
• A link to individual exons will now be available in the Region in Detail
• Highlighting of the current feature can now be disabled

Updated gene sets and annotations

• Zebrafish gene set will be updated to include manual annotation from Havana
• RNASeq data for mouse will be added
• Caenorhabditis elegans reference annotation will be updated to Wormbase WS240
• Saccharomyces cerevisiae assembly will be renamed from EF4 to R54-1-1 and liftover mapping will be added

Variation data imports and updates

• Human phenotype data will be updated
• HGMD-PUBLIC data will be updated from release 2013.9 with regulatory data for human
• Mouse phenotype data from IMPC (International Mouse Phenotyping Consortium) will be imported
• The latest sequence variants from dbSNP build 139 for dog, horse, opossum, platypus and zebra finch will be imported.
• Variation data for turkey from dbSNP build 139 will be added
• Variation citations will be updated from EPMC and UCSC

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’s new in e!74?

• Updated human GENCODE release 19 and mouse GENCODE release M2 gene sets including manual annotation from Havana
• New assembly patches for human (GRCh37.p13) and mouse (GRCm38.p2)
• dbSNP Build 138 data for human, mouse and cow
• New secondary structure models for ncRNAs
• New matrix configuration for RNASeq models for human, sheep and opossum
• Updated human phenotype data
• COSMIC version 67 and update of COSMIC structural variants
• Variation data for sheep from dbSNP build 128 as well as imported sheep genotyping chips
• Added mouse phenotype data from IMPC (International Mouse Phenotyping Consortium)
• New species: sheep, cave fish and spotted gar
• Updated armadillo assembly to Dasnov3.0. Tissue-specific gene models with indexed BAM files are also provided.

New matrix configuration for RNASeq models

To make management of large number of tracks easier, configuration for RNASeq models for human, sheep and opossum now appears as a matrix.

New page displaying ncRNA secondary structure

The secondary structure of ncRNAs is now displayed on the Gene Summary page. Clicking on the “enlarge” link below the image will take you to a new page showing more detail of the structure, including base pair mutations and sequence degeneration.

New species

We are happy to announce annotation for three new species in this release.

The sheep (Ovis aries) assembly, Oar_v3.1 (GCF_000298735.1), was produced by the International Sheep Genomics Consortium (ISGC). Sheep is an important livestock animal reared for meat, fleece and milk. We have generated BAM files and RNASeq-based gene models for  91 samples, including a wide range of tissues between a trio (ram, ewe and lamb), 7 tissue types from the reference sheep and different tissue samples from different breeds.

The blind cave fish (Astyanax mexicanus) assembly, AstMex102 (GCA_000372685.1), was produced by the Washington University. This species is used as a model organism in the study of retinal degeneration. We have generated a BAM file and RNASeq-based gene models for cave fish.

The spotted gar (Lepisosteus oculatus) assembly, LepOcu1 (GCA_000242695.1), was produced by the Broad Institute of MIT and Harvard. Spotted gar is biologically similar to other fish, yet its genome is surprisingly similar to human. It is therefore used as a model for understanding human development, and represents a connection to medical models in the teleost clade. We have generated BAM files and RNASeq-based gene models for 10 different tissues.

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

Ensembl 74 is scheduled for release in December 2013. Highlights for the coming release include:

Updated gene sets

• Human GENCODE release 19 and mouse GENCODE release M2: manual annotation from Havana will be updated and merged with Ensembl automatic annotation to produce the next gene sets for GENCODE
• Assembly patches will be added and annotated for human (GRCh37.p13) and mouse (GRCm38.p2)
• Armadillo assembly will be updated to Dasnov3.0 and include RNAseq data

Variation data imports and updates

• The latest sequence variants from dbSNP build 138 for human, mouse and cow will be imported.
• COSMIC version 67 will be imported and COSMIC structural variants will be updated.
• Mouse phenotype data from IMPC (International Mouse Phenotyping Consortium) will be imported.
• Variation data for Sheep from dbSNP build 128 and available genotyping chips will be imported.
• Variation citations will be updated and include, for the first time, data mined by UCSC.

New species (all with RNASeq data)

• Sheep (Oar_v3.1)
• Cave fish (AstMex102)
• Spotted gar (LepOcu1)

New web features

• The Ensembl species list page will contain an exportable table with sortable columns
• Secondary structure of RNAs will be on the Gene Summary page
• The gene phenotype view will show phenotypes associated with orthologues of the current gene.

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’s new in e!72?

• Updated patches for the human assembly (GRCh37.p11)
• New variation citation page and individual genotype search box
• Addition of phenotype association data from OMIM and Orphanet as well as data from the GIANT and MAGIC association studies.
• Imported HGMD-PUBLIC data from release 2013.1 with regulatory data for human.
• Import of COSMIC version 64 and update of COSMIC structural variants
• Updated HAVANA manual curation for human and mouse.
• Import of the genotypes from the Mouse Genomes Project, SNP Release Version 3.
• Updated CCDS sets and cDNA alignments for human and mouse.
• Addition of variation data for gibbon.
• Updated mitochondrial sequence and annotation for several species including alpaca, lamprey, platyfish and xenopus.

New variation citation page and search box

We have added a new page listing the publications where a variation has been cited. This information can also be retrieved in the new variation citation filter and attribute section of the Variation mart.

A form to search an individual is now available in the “Individual genotypes” page located on the variation tab.

Upload VEP output

We have added the ability to upload a VEP output file to the website through the standard upload form. This allows you to re-upload previously calculated consequences, whether from a previous run of the VEP online tool that you have deleted from the website, or an output file from the standalone script (subject to our usual 5MB upload limit).

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

Ensembl 72 is scheduled for release in June 2013. We expect this release to include, among other things:

• Updated patches for the human assembly (GRCh37.p11).
• Imported HGMD-PUBLIC data from release 2013.1 with regulatory data for human.
• Import of COSMIC version 64 and update of COSMIC structural variants.
• Addition of phenotype associations data from OMIM and Orphanet and data from GIANT and MAGIC association studies.
• Updated HAVANA manual curation for human and mouse.
• Import of the genotypes from the Mouse Genomes Project, SNP Release Version 3.
• Addition of variation data for Gibbon.
• Addition of a form to search an individual in the “Individual genotypes” page (variation tab) and a new page listing the publications where the variation has been cited.
• Updated CCDS sets and cDNA alignments for human and mouse.
• Updated mitochondrial sequence and annotation for several species including alpaca, lamprey, platyfish and xenopus.

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 lastest Ensembl update (e!71) has just gone live!

What’s new in e!71?

• SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog. Find them in the variation table, through the VEP or using the variation API.
• New views and web features
  • New “clinically associated” summary track on Region in Detail for human variation
  • Expression view
  • Transcript comparison view
  • Scrollable overview on region in detail
• Import of COSMIC version 63 and update of COSMIC structural variants
• Updated gene sets
  • Human and zebrafish, with manual annotation from HAVANA
  • Anole lizard, including RNAseq data
• Variation data available in VCF format on the FTP site
• Phenotype data for some farm animals
• New assemblies
  • Chicken (Galgal4), including RNAseq
  • C. elegans (WBcel235)

New views and web features

We have added a new “clinically associated” summary track for Human showing ClinVar variants.

We have added a new expression view to the set of gene-based displays, listing the available RNASeq data for a given species, with links through to Region in Detail that turn on a set of RNAseq tracks for a given tissue.

A new transcript comparison view allows comparison of transcript sequences for a gene.

A scrollable overview panel (supported by most updated browsers) is now available on the Region in detail view.  If you do not have a compatible browser you will see the static Region in detail view, and there is an option available to switch between scrollable and static images for supported browsers.

The RNASeq data supporting the introns of RNASeq genes is now shown on the Supporting evidence panels for those transcripts. The display distinguishes between alignments that support canonical and ones that support non-canonical splice sites.

New Assemblies

We are happy to introduce two assembly updates for this release.

The chicken (Gallus gallus) genome, Galgal4, was produced by the International Chicken Genome Sequencing Consortium. In addition to being important agriculturally, the chicken is an important model organism for biomedical research, development, and ageing. The chicken is also one of the primary models for embryology and development, the study of viruses, and cancer.

The WBcel235 assembly of C. elegans (Caenorhabditis elegans) has been imported from the WS235 release of WormBase. C. elegans provides a model for complex organ systems, as well as developmental biology and genetics.

Ensembl release 71 is scheduled for release in April 2013. We expect this release to include, among other things:

• SIFT scores for all possible changes to the proteome in human, mouse, zebrafish, pig, cow, chicken, rat and dog
• New “clinically associated” summary track on Region in Detail for human
• VISTA Enhancers updated for human and mouse to the latest release (28/1/2013).
• New DNA methylation data
• New whole genome bisulphite sequencing (WGBS) sperm data set for human
• Several reduced representation bisulphite sequencing (RRBS) sets for mouse
• Import of COSMIC version 63 and update of COSMIC structural variants
• Updated gene sets
• Human and zebrafish, with manual annotation from HAVANA
• Anole lizard, including RNAseq
• Updated cDNA alignments for human and mouse
• Phenotype data for some farm animals
• New assemblies
• Chicken (Gallus_gallus4.0), including RNAseq
• C. elegans (WBcel235)

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.

We are pleased to announce release 70 of Ensembl.

What’s new in e!70?

• New web features (sharing and streamlined interface to add your data to Ensembl).
• Updated patches for the Human assembly (GRCh37.p10) and inclusion of patches for the Mouse assembly (GRCm38.p1).
• Reanalysed Human BodyMap data from Illumina using the recently updated RNASeq pipeline. The BodyMap BAM files can be downloaded from our ftp site.
• Imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human.
• Updated HAVANA manual curation for Human and Mouse.
• A new regulatory build for Mouse including a much broader coverage for the Embryonic Fibroblast (MEF) build and additional data on other cell types.
• New assemblies for Rat (Rnor 5.0) and Cat (Felis catus 6.2) and a new geneset for Fruitfly (FlyBase version 5.46).

Sharing pages and images and other web integration

Sharing is now enabled on Ensembl views. We have added a share icon in the toolbar above configurable images and a share button in the left menu on each page. Click on the share icon or button to send the link to a collaborator or colleague.  This works with uploaded data, and is a quick way to share your own data track with others. More information can be found in our FAQ.

We have merged the web interfaces for uploading your data and attaching it via a URL into a single form that changes as you select options. Click “Add your Data” to get started.

For the convenience of our Chinese users, if your IP address is based in China you will be served the Youku versions of our video tutorials instead of the YouTube ones.

Sequence Variation

We have new Human structural variants from COSMIC release 61. Sequence variation for Mouse and Cow have been updated to dbSNP 137. Rat and Cat have been remapped to the new assembly. Also we have imported HGMD-PUBLIC sequence variation data from release 2012.3 with regulatory data for Human.

New Assemblies

We are happy to introduce two major assembly update for this release.

The Norway rat (Rattus norvegicus) genome, Rnor_5.0 was provided by the Rat Genome Sequencing Consortium. Rat models have been used to advance medical research in many areas like cardiovascular diseases, psychiatric disorders, neural regeneration, diabetes, cancer, wound and bone healing. Drug development also relies on rat models to demonstrate therapeutic efficacy and assess toxicity of drug compounds prior to human clinical trials.

The Felis_catus-6.2 assembly of the cat (Felis catus) genome was produced by the International Cat Genome Sequencing Consortium. The domestic cat is a significant model organism for biomedical research, especially in infectious disease research, and has aided human disease in research fields including neuroscience, behavioural biology, reproductive physiology and endocrinology.

Ensembl release 70 is scheduled for release in January 2013.

We expect this release to include, among other things:

• Updated patches for the Human assembly (GRCh37.p10) and inclusion of patches for Mouse assembly (GRCm38.p1).
• Imported HGMD-PUBLIC data from release 2012.3 with regulatory data for Human.
• An increased number of human phenotype annotations.
• Updated human and mouse CCDS sets.
• An update of the HAVANA manual curation for human and Mouse.
• Imported COSMIC’s latest release and update of COSMIC’s structural variants.
• Human BodyMap data reanalysed using the recently updated RNASeq pipeline.
• The latest sequence variants from dbSNP build 137 for Mouse and Cow.
• A new regulatory build for Mouse including a much broader coverage for the Embryonic Fibroblast (MEF) build and additional data on other cell types.
• New assemblies for Rat (Rnor 5.0) and Cat (Felis catus 6.2).
• Updated Drosophila geneset to FlyBase version 5.46.

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.