The latest Ensembl update (e!69) has just gone live!

What’s new in 69?

• Human dbSNP release 137 and Human structural variants from COSMIC release 60.

• 1000 Genomes phase 1 data for the structural variation set and new studies for Human and Mouse.

• DNA methylation data from multiple human and mouse cell lines (including ES cells for both species) and data from ENCODE.

• Updated HAVANA manual curation for Human and Zebrafish and the first inclusion of HAVANA manual curation for Ensembl genes in Pig.

Scrollable region view and other new web displays

Other exciting news for this release is a new scrollable region view (supported by most updated browsers).  Find out more about it in this video.

We offer a new display for species with phenotype data (currently only Human) which lists all available phenotypes in alphabetical order. This will make it easier to search the website for a phenotype or disease of interest.

The species home page has been redesigned to incorporate more links to our content and help you quickly find what you need. The original page is still available under the “More about this gene build” link under the “Gene annotation” section.

We have also added a gene Gain/Loss tree view produced using CAFE analysis, and an improved legend for gene trees to make them clearer.

New Species

We are happy to introduce two new species for this release.

The Ferret (Mustela putorius furo) genome was produced by the Broad Institute.  Ferret has become an important biomedical model for  respiratory diseases such as influenza (including H1N1), cystic fibrosis, and SARS. We have generated BAM files and RNASeq-based gene models for a range of samples including embryo and adult tissues, and tissue samples post infection with influenza.

The Southern Platyfish (Xiphophorus maculatus) assembly was provided by the Genome Institute, Washington University School of Medicine and comprises 20,640 unplaced scaffolds. Platyfish is of interest for development of malignant melanoma when crossed with other members of the Xiphophorus family, and the family is used as a model for the study of hereditary cancer. RNASeq data was included in the genebuild and we provide a BAM file and a set of RNASeq-based gene models.

We are pleased to announce release 68 of Ensembl.

This release includes the new mouse assembly (GRCm38) as well as updated patches for the human assembly (GRCh37.p8).  We introduce the Chinese softshell turtle (Pelodiscus sinensis) as a new species and update the Dog genome to CanFam3.1. The ground squirrel has been renamed to Ictidomys tridecemlineatus in line with recent taxonomic reassessments.

Sequence Variation

We have new Human structural variants from COSMIC release 59. Structural variation for Human and Mouse have been updated and new studies have been added. Sequence variation for Dog  has been updated to dbSNP 131 and remapped to the new assembly.  Mouse variations have also been remapped to the new assembly.  Structural variation data are now available for Zebrafish (Danio rerio), Cow (Bos taurus) and Horse (Equus caballus). In addition, we have moved to using Sequence Ontology terms to describe consequences in Ensembl. The old Ensembl terms will still be available however we encourage users to use the new ones; we hope they become standard across all browsers.

New Mouse assembly

The high coverage assembly GRCm38 of the Mouse (Mus musculus) genome was produced by the GRC (Genome Reference Consortium). This new assembly is composed of 21 chromosomes and 22 unplaced scaffolds. Similar to the human genome assembly, the Genome Reference Consortium will be releasing additional sequence for GRCm38 in the form of minor releases (patches) in the future. Just as for the human genome, we will provide gene annotations and pairwise alignments for these regions.

New Species

The Chinese softshell turtle (Pelodiscus sinensis) assembly was produced by the RIKEN institute. The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for Chinese softshell turtle from RIKEN and BGI Institutes, the final gene set comprises of models based orthologous proteins from the vertebrate division of UniProtKB in addition to models from RNASeq data.

Website design update

In other news, starting with this release we will be incrementally refreshing the design of the Ensembl web template to improve its usability. The first stage involves minimal changes designed to make the pages tidier and more readable, without altering current functionality. Our only new design feature this release is an icon bar attached to the dynamic images, which replaces the “Export Image” button.

The latest Ensembl update (e!67) has just gone live!

This release includes one new species; Nile tilapia (Oreochromis niloticus) as well as the patches for the human assembly (GRCh37.p7) and an assembly update for two species, Pig (Sscrofa10.2) and Squirrel (SpeTri2.0).

Sequence Variation

Human structural variants from COSMIC (release 58) have been imported in Ensembl; view them in our new somatic structural variation track.  We now provide 1000 genomes phase 1 genotype data.  For other species, sequence variation for Pig, Zebrafish, Rat, Chimpanzee and Orangutan have been updated to dbSNP 136.  Variation and structural variation data are now available for Macaque (Macaca mullatta).

Patches and Haplotypes

Compare patches and haplotypes along the reference sequence for human in our newly renamed, “Region Comparison” view (previously “Multi-species view”) on the browser.  Jump there from a patch or haplotype region on Region in Detail, as in the image.

New Species

The Nile tilapia (Orenil1.0) assembly was provided by the Broad Institute. Illumina technology was used to produced this high quality draft. A mixed approach was used for the genebuild using the RNA-Seq pipeline and the Ensembl pipeline.

Virtual Machine

In other exciting news, Ensembl now has a virtual machine with all the Ensembl APIs and the VEP (Variant Effect Predictor) pre-installed  and ready to use. Just make sure you have virtualization software on your machine, download the Ensembl pre-configured file and install it. Detailed information can be found in the Ensembl Tools section.

More news is available on the Ensembl website.