What’s new in e79:

• Human: genes updated to GENCODE 22, and new assembly patches (GRCh38.p2)
• Comparison of imported human RefSeq transcript set to Ensembl models
• New interactive gene gain/loss tree view
• Global Alliance REST endpoints
• NextGen project genotype sheep data from Iranian and Moroccan populations

Human update

The human gene set now corresponds to GENCODE 22 while the assembly has been updated to include new assembly patches for GRCh38.p2.

Comparison of human RefSeq transcripts to Ensembl models

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.

Gene gain/loss tree view

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.

Global Alliance REST Endpoints

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.

Import of NextGen project sheep genotype data

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.

Other news

• Updated human HAVANA annotation in Vega
• Import of phenotype and disease data from the Rat Genome Database (RGD)
• RefSeq GFF3 annotations for majority of Ensembl species
• Addition of non-coding genes to the vervet-AGM gene set
• Updated APPRIS flags for human, mouse, rat, zebrafish with addition of pig
• Assembly and gene set update for Drosophila to BDGP6 (FB2014_05)

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!).