12 July, 2011

Ensembl Genomes Release 10

The Ensembl Genomes Project is pleased to announce release 10 of Ensembl Genomes.

The main highlights of this release are:

* Software migration to Ensembl 63

* Trypanosoma brucei, a causative agent of Human African trypanosomiasis, or sleeping sickness added to Ensembl Protists.

* Ustilago maydis (Plant-pathogen interaction model), Puccinia triticina (wheat rust fungus) and Nectria haematococca (Plant pathogen) added to Ensembl Fungi.

* Latest 1001 Genomes release included for Arabidopsis thaliana, together with 5 additional gene models from TAIR10.
Projection of GO terms from Arabidopsis thaliana and Oryza sativa japonica to other species based on homology, also added for Ensembl Plants.

17 February, 2011

The Ensembl blog is moving!

We have now moved our blog to an independent server that will allow us more control. Forthcoming new features include a workshop calendar, and some content such as our development roadmap will also be moved from the main Ensembl website to the blog site, where they are easier for us to update.

New Ensembl blog

Please update your bookmarks and RSS readers to the new address, as no further posts will be made here.

See you on the new site! You will be redirected in 4 seconds.

09 February, 2011

New Ensembl Genomes release expands the metazoa

I'm going to be blogging a bit more about the recent Ensembl 61 release and the Ensembl Genomes 8 release - lots and lots of goodies in both these releases - web site tweaks (some of the them totally critical for generating good displays), the new "favourite tracks" feature, and impressive content changes.

I'll start today on content changes, and in Ensembl Genomes 8 there are some important genome additions. Some come from Paul Kersey's new collaboration with PhtyoPathDB - more on that in a later post - but top of my excitement has been the diversity in metazoa. The Ensembl Metazoa team has added Sea Urchin, Sea Anemone, the rather weird primitive animal, Trichoplax adhaerens (also called the "carpet" organism) and the blood fluke, Schistosoma mansoni. The motivation of bringing these organisms in is to broaden our phylogenetic tree and comparisons we can provide across all of life. So for example for the drosophila Twist

One can now see the deep tree for this across metazoa:

For example, there is a deep ortholog to Trichoplax:

which seems to predate the split of some of these Helix Loop Helix proteins, whereas
there are other members of the family which have paralog in Trichoplax

meaning that there seems a fundamental split in this developmentally key
transcription factor. This is just one of many interesting gene trees that
one can look at using this resource...

Happy browsing/data mining!

Ensembl Genomes Release 8

The Ensembl Genomes Project is pleased to announce release 8 of Ensembl Genomes (http://www.ensemblgenomes.org/).

The main highlights of this release are:

Software migration to Ensembl 61

New Pan Compara database consisting a selection of vertebrate genomes from Ensembl 61 and genomes from Ensembl Genomes 8 (incorporating 8 new species), giving a species total of 313.

3 oomycete genomes added to Ensembl Protists, including Phytopthora infestans and Phytopthora ramorum responsible for potato blight and Sudden Oak Death disease respectively.

5 genomes added to Ensembl Metazoa, including Strongylocentrotus purpuratus (Echinodermata) (sea urchin), Apis mellifera (Arthropoda) (honey bee) and Nematostella vectensis (Cnidaria) (sea anemone).

For further details please visit the individual homepages:

02 February, 2011

Favourite tracks in 61

Ensembl 61 has gone live. In displays like gene summary and region in detail, favourite tracks can be turned on. To do this, open the configuration panel (click on configure this page in the left hand menu). Activating a star by clicking on it will place that track in the favourites menu (shown by an arrow in the diagram).

Hover over any track name in these views to view information about the data, change the display, or turn the track off. Turning on tracks must still be done with the configuration panel.

We hope this helps ease of navigation. Read about other updates in 61, such as our new species, Turkey, in the news. The Ensembl Team

28 January, 2011

New genebuild summaries now available

We are pleased to announce new documentation, specific for describing the gene annotation methodology and results for particular species.

Ensembl gene annotation is a multi-step process which usually takes several months to complete for one species, and is termed the genebuild. In order to provide our users with more information on the data resources used and decisions made during the genebuilding process, we are introducing a new genebuild summary PDF document for each new genebuild, starting from early February 2011 with Ensembl release 61. Each document includes details on not only the alignment programs and data filtering parameters used, but also statistics on the number of protein/cDNA/EST sequences used at different stages of the genebuild. For example, users will be able to find out how many protein sequences were retrieved from public repositories (RefSeq and UniProt) at the beginning of the genebuilding process, how many of these proteins aligned to the genome by various algorithms at different stages of the build, and how many remain in the final gene set as supporting evidence for genes. For human, mouse and zebrafish, the process of merging Ensembl and Havana annotations is also explained.

The genebuild summary will be available for six species: the Anole lizard, Marmoset, Mouse, Panda, Turkey and Zebrafish. More genebuild summaries will be available in the future when genebuilds of existing species are being updated, or when new species are being annotated. You can download the document via a link found near the bottom of the "Description" page for each species. Just click on the species of interest from the home page, to open its description page.