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, 43 (Database issue), D662-9

Ensembl 2015


Ensembl 2015

Fiona Cunningham et al. Nucleic Acids Res.


Ensembl ( is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site ( Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (, which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page ( under an Apache 2.0 open source license.


Figure 1.
Figure 1.
Ensembl ‘Region in Detail’ view showing the improved annotation of SLC38A3 in GRCh38, regulatory region information, default variation track and Age of Base track. (a) The GRCh38 assembly has resulted in an improved annotation of many genes compared to GRCh37.p13. Here we show the SLC38A3 gene as an example, where updates to the genome sequence now allow an open reading frame to be annotated. SLC38A3 is viewable in the GENCODE Basic track which shows only selected transcripts per gene. (b) The following regulatory tracks are shown from our new Ensembl Regulatory Build: MultiCell regulatory features (regions that are assigned a function that is independent of the cell type); cell type-specific regulatory data (for 4 selected cell types, out of 18 available - a regulatory feature is shaded in grey if it is inactive in the corresponding cell type, below each cell type is the cell type-specific segmentation track); H1ESC cell line Whole Genome Bisulphite Sequencing; Fantom5 (enhancers and promoters defined by the FANTOM5 project). (c) A track for variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% across any population is now on by default. The variants are colour coded by most severe consequence type (see Variation Legend in the lower part of the image). (d) Age of Base track: Each base pair that differs by a substitution in the human genome is classified as an event according to when it occurred: before the primate evolutionary branch (grey), in the primate-specific branch (blue), in the human-specific branch and is now fixed (red) or in the human-specific branch as a segregating variant (yellow).
Figure 2.
Figure 2.
Improved VEP web tool and interface: The output is summarized using pie charts and statistics. Additionally, the results preview can be filtered on any output column. The output data can be filtered and downloaded for further analysis.

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