Ensembl 2016

Abstract

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

Figure 1.

Ensembl's location view showing the drawing of long-range interaction arcs and new region marking tool. The grey boxes indicate HindIII fragments and the arcs represent selected significant interactions between promoters and their distal interacting elements, measured using high resolution Capture Hi-C in the GM12878 lymphoblastoid cell line and displayed for the GRCh38 assembly (43). The summary Ensembl Regulatory Build and the GM12878 specific regulatory activities are also shown. Our region marking tool is shown as a light grey box surrounding the transcripts PSMD9 and RP11–87C12.2.

Figure 2.

The new Ensembl mobile site showing BRCA2 and detailing available synonyms, genomic location and links to external resources such as CCDS. Search is available in the top right corner on all mobile site pages and each page has the ability to be shared over social media and email.