Marker portal

The prototype ENA Marker Portal has been launched as an entry point into sequence data arising from the sequencing of marker loci across multiple species and strains. Marker data can be filtered taxonomically and by locus name, for which we have implemented a system that resolves the diversity of labels that are typically applied to the same locus across taxa and studies.

Using the ENA Marker Portal

To perform a search for marker sequences, go directly to the Marker Portal or select the marker domain from Advanced Search.

Select the marker of interest and the taxon of interest. If you wish to search for marker sequences over a portion of the taxonomic tree, check “Include subordinate taxa”.

After hitting the search button, you will get a list of available results. Expand the coding results and you will see a selection of three different types of results: records, report and marker.

Records tab

The records tab provides the traditional list of ENA accessions and descriptions, with links to each record page in the browser. There are also options to display, or download, the full (or partial) list of sequences in text, XML or FASTA formats.

Report tab

The report tab shows a table of metadata for each record. A subset of the available metadata columns is displayed by default and this can be altered by choosing “Select columns”. The selected columns can also be displayed or downloaded in tab separated text format.

Marker tab

The marker tab shows a visual rendering of the portion of the taxonomic tree that was searched. For display reasons, this has been limited to a maximum depth of three tax nodes. Each taxon is coloured based on the number of sequences available for each taxon (relative to the search conditions, NOT with respect to overall marker sequences available in ENA). A grey taxon has no marker sequences and the remaining are coloured from light to dark blue with a darker colour meaning more available sequences. Hovering the mouse over any taxon in the tree will display the full scientific name, with the number of available sequences, to the right of the graphic. All counts used for the tree are based on sequences available for the taxon in question as well as all subordinate taxa. While the graphic is limited to a maximum depth of three nodes, the full taxonomic tree for the result can be obtained via the links to display, or download, the result in text format.

Latest ENA News

20 Aug 2014: Read data through Globus GridFTP
Read data can now be downloaded using Globus GridFTP through ebi#ena Globus Online public endpoint.

18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

1 Jul 2014: ENA release 120
Release 120 of ENA's assembled/annotated seqences now available

23 May 2014: Change to date format for advanced search
From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).

20 May 2014: Update to the ENA SAMPLE checklist
From 10th of June 2014 the ENA SAMPLE checklist XML will be updated and the older version will be deprecated.