25 January, 2009

Upcoming workshops February 2009

In February we will have the following Ensembl workshops:

10 Feb: Browser workshop at the Institute for Animal Health in Pirbright
11 Feb: Browser workshop at the Institute of Molecular Genetics in Prague, Czech Republic
12 Feb: Developers workshop at the Institute of Molecular Genetics in Prague, Czech Republic
23 Feb: Ensembl module in the EBI Roadshow at the Cyprus Institute of Neurology & Genetics in Nicosia, Cyprus
24-25 Feb: Developers workshop at the e-Science Centre in Edinburgh
26 Feb: Browser workshop at the Institute for Animal Health in Compton

For details about these and other upcoming workshops, please have a look at the complete list of Ensembl training events.

21 January, 2009

How to get all the orthologous genes between two species

Many users ask us about how to download data from ensembl. Usually, the answer is using BioMart. Comparative genomics data are also available in the standard Mart for your favorite species. For instance to get all the human-mouse orthologs, one can select the human dataset, filter all the genes with no mouse orthologs and choose to output the mouse orthologs for all the resulting genes.

Here is how to get these data in 10 simple steps
1. Go to: http://www.ensembl.org/biomart/martview
2. Choose "Ensembl 52"
3. Choose "Homo sapiens genes (NCBI36)"
4. Click on "Filters" in the left menu
5. Unfold the "MULTI SPECIES COMPARISONS" box, tick the "Homolog filters" option and choose "Orthologous Mouse Genes" from the drop-down menu.
6. Click on "Attributes" in the left menu
7. Click on "Homologs"
8. Unfold the "MOUSE ORTHOLOGS" box and select the data you want to get (most probably the gene ID and maybe the orthology type as well).
9. Click on the "Results" button (top left)
10. Choose your favorite output

Here is the preview of the results:

Other people may prefer to use our Compara Perl API or get the data directly from the Compara DB. These options are also available.

13 January, 2009

Extending Ensembl

Following a recent thread in our ensembl-dev mailing list, we can point our users to a recent post in the Gramene blog (a resources for grass genomes maintained at CSHL). This framework extends Ensembl with a data resource to browse several plant species: maize (Zea mays), rice (Oryza glaberrima and Oryza rufipogon), sorghum (Sorghum bicolor), the model organism Arabidopsis thaliana, grape (Vitis vinifera), and poplar (Populus trichocarpa); with comparative maps for additional species such as wheat (Triticum aestivum), barley (Hordeum vulgare) and oat (Avena sativa).

You can find some sample scripts to load an Ensembl species database from scratch, here.

Thanks to our colleagues at Gramene.

11 January, 2009

Ensembl Website road map...

We hope you like the new Ensembl website - we have had quite a lot of feedback about the system, and are digesting this to see how and where we can make the site more easy to use.

Missing features

We know there are a number of features which were in the webcode prior to the revamped version 51 that we are working on.

  • AlignSliceView [target e!53]
  • MultiContigView [target e!54]
  • CytoDump [will be released in e!53 as part of the export module]
  • DotterView
  • HistoryView - "ID liftover" [target e!53/4]
  • AssemblyConverter - "location liftover" [target e!53/4]
  • Drawing code tracks, e.g. rat QTLs, protein co-ordinate based DAS tracks [target e!53]
  • User gene annotations [target e!54]
New developments

We have a number of new "web" developments in the pipeline - some of these are listed below:
  • Extended configuration panel - searching for tracks, show currently active etc [target e!53]
  • Extended configuration panel - re-ordering tracks etc [target e!53]
  • Extended configuration panel - further configuration options - colour, depth, more display options, label options [target e!54/5]
  • New BLAST/BLAT interface [target e!55/6]
  • Re-write of the vertical drawing code to allow high quality PDF/PS/SVG karyotype and chromosome images to be produced.
  • Further work on export - finer configuration of what to export, exporting in multi-regions, integration with "user data"

09 January, 2009

Ensembl 53

We are already working on our next release (out late in February 2009) which will come with the following:


  • New species added to our set: sloth (Choloepus hoffmanni), Anolis lizard (Anolis carolinensis) and zebrafinch (Taeniopygia guttata).
  • Updated marker information for human, cow, dog, horse, chicken, macaque, mouse and Medaka.
  • Updated manual annotation for mouse from VEGA.
Comparative Genomics
  • Pairwise alignments with the new species (human/sloth, zebrafinch/chicken, lizard/chicken).
  • New 31-way eutherian mammal alignment using these 2x genomes (based on the 9-way Enredo-Pecan-Ortheus multiple alignments): elephant (Loxondonta africana) , armadillo (Dasypus novemcinctus), tenrec (Echinops telfairi), rabbit (Oryctolagus cuniculus), guinea pig (Cavia porcelus), hedgehog (Erinaceus europaeus), shrew (Sorex araneus), microbat (Myotis lucifugus), tree shrew (Tupaia belangeri), squirrel (Spermophilus tridecemlineatus), bushbaby (Otolemur garnetii), pika (Ochotona princeps), mouse lemur (Microcebus murinus), cat (Felis catus), megabat (Pteropus vampyrus), dolphin (Tursiops truncatus), alpaca (Vicugna pacos), kangaroo rat (Dipodomys ordii), hyrax (Procavia capensis), tarsier (Tarsius syrichta), gorilla (Gorilla gorilla) and sloth (Choloepus hoffmanni).
  • The current clustering will be replaced by a hierarchical clustering sparse graphs (hcluster) for our trees.
Variation and Functional Genomics
  • An improved array mapping environment integrates genomic and cDNA mappings, supporting multi-species databases.
  • We'll link to Genome Wide Association from the NHGRI catalogue (Hindorff et al.)
  • Genotype data for mouse (reference strain C57BL/6) will be included.
  • Update of variation for dog, chicken and platypus.