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How can I download all the gene/transcript/protein sequences for a species? Do I use BioMart?

While BioMart can export sequences, the entire set for any species can be downloaded directly from our ftp site. Please use this method of download, as BioMart cannot handle the very large query of a whole gneome/transcriptome/proteome.

If you do need a customised sequence header, consider splitting the BioMart query into chromosomes. Make sure the compressed webfile/notify by email option is selected.

For BioMart tutorials, see our video on YouTube or YouKu.


If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.