We are pleased to announce that we are now providing access to the ENCODE integrative analysis data from within Ensembl. These analyses bring together a multitude of experiments targeted at determining functional elements in the human genome sequence. This data is provided from an external source (a track hub at the EBI).  Although the Ensembl code supporting track hubs is still in preliminary form, we considered this ENCODE set sufficiently important to release the code early to enable us to provide access to this set.

Important: Please read the instructions below before activating this data!

As this dataset is very large (over 2800 tracks) it is not configured on by default in the Ensembl browser. To add the ENCODE hub tracks, click on the link below. Warning: users of IE6 or IE7 should not do this because performance in those browsers is inadequate and the page will not load.

Link to add ENCODE integrative analysis hub

No tracks from the hub are switched on by default. To turn on tracks from ENCODE, go to ‘Configure this page’ and click on one of the submenus under ‘ENCODE data’, for example ‘ENCODE genome segmentations’. It will take a few seconds to bring up the track list. Then switch tracks on or off by clicking on the box next to the track name and choosing a track style. For genome segmentations the ‘Compact’ track style looks good.  More information on configuring the display is available in our recently released video tutorial on region in detail view. Here’s an example of a region showing a few ENCODE tracks (HepG2 and K562 genome segmentations and cytosolic RNASeq tracks):

If you no longer need access to the ENCODE set of tracks, the hub can be turned off by going to the ‘Manage your data’ link in the left hand menu, and clicking on the trash bin icon for the ‘ENCODE data’ source to delete it from the ‘Configure this page’ menu.

We will be working over the next few months to extend our track hub support, including improving the performance and adding features of configuration interface.

Ensembl announces the release of http://ncbi36.ensembl.org. This Ensembl site is for users who still need access to the NCBI36 human assembly. It is actually a complete copy of the Ensembl 54 release which was the last Ensembl release containing NCBI36.

Although access was already possible through the Ensembl archive sites, the new ncbi36.ensembl.org site will provide better performance because it is running on separate hardware. Also ncbi36.ensembl.org provides Blast/Blat search support which the archives do not.

The main reason we have provided a dedicated site for NCBI36 is for two large projects (Encode and 1000 Genomes) which have some of their data aligned on this assembly. ncbi36.ensembl.org will only be up for as long as there is significant need for it. We will be reviewing usage in Spring 2010 and currently plan to remove the site by Summer 2010. After that time users will still be access the NCBI36 assembly via the archive sites, there just won’t be a dedicated site for it anymore.