ENA data can be browsed and retrieved in XML, HTML, fasta, fastq and flat file formats using the ENA Browser which can be used both interactively and programmatically through REST URLs. In 2010, we extended the ENA Browser to cover EMBL-Bank and Trace archive records and introduced several improvements including a graphical EMBL-Bank annotation and assembly viewer and intuitive navigation between different ENA data classes. For full details of the ENA browser URL syntax please refer to: http://www.ebi.ac.uk/ena/about/page.php?page=browser
. For example, the following URL returns the complete mitochondrial genome for ‘Ursus spelaeus’ (cave bear) (6
(). Data can be queried using the EB-Eye free text search functionality available in the header section of all EBI web pages (7
). ENA results are available under the ‘Nucleotide Sequences’ category and linked to the ENA Browser. Free text search is also available from the ENA home page: http://www.ebi.ac.uk/ena
The complete mitochondrial genome for Ursus spelaeus (cave bear) from the Max Planck Institute for Evolutionary Anthropology submitted to EMBL-Bank in 2010.
Rapid and comprehensive sequence similarity searches against ENA data are supported through a new service based on Exonerate (8
) technology: http://www.ebi.ac.uk/ena/search/
(Goodgame, N., manuscript in preparation). All nucleotide sequences archived by the INSDC and made available as part of EMBL-Bank are covered by our service. This includes all ENA sequences except raw reads from the Trace Archive and SRA. Experimental search support for a limited number of raw reads is provided through De-Bruijn servers based on Velvet (9
), using the Exonerate client-server protocol and being fully integrated with our search service. This search is available by selecting the ‘Experimental De Bruijn search’ option from the search page. The EMBL-Bank sequence search service is currently being expanded for more specific purposes according to community requests.