Archive Ensembl HomeArchive Ensembl Home
Home > Help & Documentation

Projects using Ensembl

The Ensembl project is both a source of genome sequence related data ( and an open source software system that can be used to organise any such data.

User-contributed code

Whilst we have developed a comprehensive Perl API in-house, we welcome contributions in other programming languages from the community.


A Ruby API has been developed by Jan Aerts. A small example, showing what it can do (including coordinate transformation and reflecting on the types of associations for a given class) can be found on the wiki page.

Note that we do not support these user-contributed packages - please contact the original developer if you have any questions or comments.

Ensembl-powered Websites

Some projects make use of the Ensembl software system, or are derived from it.

'Powered by Ensembl' logo

Project Description Code used
Vega Website to present curated vertebrate annotation Web front-end derived from Ensembl webcode;
Ensembl database and Perl API
VectorBase Bioinformatic Resource Centre for Invertebrate Vectors of Human Pathogens Customised Ensembl webcode, Ensembl Compara pipeline, Ensembl annotation pipeline
DeCIFR legume project Automated annotation and display of legume genomes Customised Ensembl pipeline, API, and webcode
AtEnsembl Arabidopsis thaliana genome browser Customised Ensembl pipeline, API, and webcode
Otter Database backend for interactive curation of annotation Otter is an extension of the Ensembl database schema
Gramene A Comparative Mapping Resource for Grains Customised webcode, Ensembl Compara pipeline, Ensembl database used for annotation, import of the Arabidopsis Ensembl database from NASC.
CADRE Central Aspergillus Data REpository
Sigenae Sigenae EST ContigBrowser
COSMIC (Catalogue of Somatic Mutations in Cancer) Web display of somatic sequence variant/mutation data Customised Ensembl drawing code
MVP (Methylation Variable Positions) Web display of MVPs analysed in the Human Epigenome Project. Customised Ensembl drawing code
S. pombe Gene Expression Viewer Web display of S. pombe gene expression under various environmental conditions. Customised Ensembl drawing code
PupaSuite Interactive web tool for the selection of optimal sets of SNP for genotyping purposes, with prediction of functional effect and visualisation facilities. Web front end to a CGI that uses APIs.
ISACGH Web tool to detect chromosomal copy number alterations and relate them to gene expression and gene function. Web front end to a CGI that uses APIs. DAS server.
Phylopat Web tool to show the presence or absence of certain genes or proteins in a set of eukaryote species. Uses orthologue data extracted from EnsMart.
Chromhome A database of chromosome map data, particularly chromosome painting data between species. Ensembl karyotype drawing code.

'Powered by Ensembl' logo

If you are using Ensembl code in your project, you might like to download the 'empowered' logo (high-resolution PNG, suitable for use in print).