Similar databases and browsers are found at NCBI and the University of California, Santa Cruz (UCSC).

One option is manual annotation, whereby a team of scientists tries to locate genes using experimental data from scientific journals and public databases.

Since April 2009, a sister project, Ensembl Genomes, has extended the scope of Ensembl into invertebrate metazoa, plants, fungi, bacteria, and protists, focusing on providing taxonomic and evolutionary context to genes, whilst the original project continues to focus on vertebrates.

The graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA.

Externally produced data can also be added to the display by uploading a suitable file in one of the supported formats, such as BAM, BED, or PSL.

The users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema.

Last, there is an FTP server which can be used to download entire MySQL databases as well some selected data sets in other formats.