The Ensembl 2016 report outlines updates and improvements to the Ensembl project, which provides genomic annotation, analysis, and data dissemination for a wide range of species. The project supports 87 species across its main and early access Pre! websites, with three new species added and numerous updates across supported species, focusing on the latest genome assemblies of human, mouse, zebrafish, and rat. The project also provides two data updates for the previous human assembly, GRCh37, through a dedicated website. Ensembl's tools, including the Variant Effect Predictor (VEP), have been significantly improved through integration of additional third-party data. REST is now capable of larger-scale analysis, and BioMart can deliver faster results. The website now displays long-range interactions, and a mobile-optimized website has been launched for gene, variant, and phenotype views. Ensembl generates genomic datasets through a system that analyzes, stores, and distributes data, enabling interpretation through open data release. It acts as a hub of reference data, similar to the UCSC Genome Browser and RefSeq, and distributes datasets it creates. It collaborates with projects such as ENCODE, GRC, GA4GH, and GENCODE. Ensembl's gene annotation relies on aligning cDNAs and proteins from resources like RefSeq and UniProt, alongside building transcription models from RNA-seq data. The Regulatory Build uses high-quality experimental evidence from projects like ENCODE and Roadmap Epigenomics to annotate diverse features across cell types. All gene and regulatory annotations are versioned and accessible for downstream analysis. Variation resources integrate publicly available variant data for 20 vertebrate species, with a significant increase in the number of variants. Phenotype, trait, and disease annotations for 14 species are also provided. Variation data is available for 22 species, and regulatory data for human and mouse. Comparative annotation integrates genome sequences and gene annotations of all available species into a single resource. Whole-genome alignments have been updated due to changes in rat and zebrafish assemblies. A new protein clustering and classification system is being developed, replacing the current method with a more straightforward HMM classification. The GRCh37 human assembly support includes two major releases, incorporating new data from the 1000 Genomes Project, dbSNP, and HGMD. The VEP has been enhanced to report transcript attributes and support selenocysteine modifications. The website has been improved with data export, high-resolution images, and mobile optimization. The REST API has seen substantial growth, supporting annotation using HGVS variant nomenclature and improved querying for variants. eHive, the pipeline management system, has been updated to support a generic guest language interface and improved security. BioMart databases are updated regularly, with new datasets and improved query performance. Ensembl provides external user support through training courses, online materials, and social media. The project is fundedThe Ensembl 2016 report outlines updates and improvements to the Ensembl project, which provides genomic annotation, analysis, and data dissemination for a wide range of species. The project supports 87 species across its main and early access Pre! websites, with three new species added and numerous updates across supported species, focusing on the latest genome assemblies of human, mouse, zebrafish, and rat. The project also provides two data updates for the previous human assembly, GRCh37, through a dedicated website. Ensembl's tools, including the Variant Effect Predictor (VEP), have been significantly improved through integration of additional third-party data. REST is now capable of larger-scale analysis, and BioMart can deliver faster results. The website now displays long-range interactions, and a mobile-optimized website has been launched for gene, variant, and phenotype views. Ensembl generates genomic datasets through a system that analyzes, stores, and distributes data, enabling interpretation through open data release. It acts as a hub of reference data, similar to the UCSC Genome Browser and RefSeq, and distributes datasets it creates. It collaborates with projects such as ENCODE, GRC, GA4GH, and GENCODE. Ensembl's gene annotation relies on aligning cDNAs and proteins from resources like RefSeq and UniProt, alongside building transcription models from RNA-seq data. The Regulatory Build uses high-quality experimental evidence from projects like ENCODE and Roadmap Epigenomics to annotate diverse features across cell types. All gene and regulatory annotations are versioned and accessible for downstream analysis. Variation resources integrate publicly available variant data for 20 vertebrate species, with a significant increase in the number of variants. Phenotype, trait, and disease annotations for 14 species are also provided. Variation data is available for 22 species, and regulatory data for human and mouse. Comparative annotation integrates genome sequences and gene annotations of all available species into a single resource. Whole-genome alignments have been updated due to changes in rat and zebrafish assemblies. A new protein clustering and classification system is being developed, replacing the current method with a more straightforward HMM classification. The GRCh37 human assembly support includes two major releases, incorporating new data from the 1000 Genomes Project, dbSNP, and HGMD. The VEP has been enhanced to report transcript attributes and support selenocysteine modifications. The website has been improved with data export, high-resolution images, and mobile optimization. The REST API has seen substantial growth, supporting annotation using HGVS variant nomenclature and improved querying for variants. eHive, the pipeline management system, has been updated to support a generic guest language interface and improved security. BioMart databases are updated regularly, with new datasets and improved query performance. Ensembl provides external user support through training courses, online materials, and social media. The project is funded