Ensembl just updated the live site and underlying databases to
version 53.

Some new features include ‘Active Tracks’ and a searchable ‘Configure this page’!

Go to any region of the chromosome.

Click ‘Configure this page’ at the left.

‘Active tracks’ allows you to see (and deselect) all tracks that are turned on.

‘Search display’ allows you to search for tracks in the menus. In this example, we searched for UniProt. Tracks from different menus appear.

For more updates, including new species, variations, and Amazon Web Services, see the news.

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

Data

Zebrafish
We will be releasing a new genebuild for zebrafish (with updated repeat masking) based on the latest assembly Zv8. Thus, we’ll have a new gene set (with new probeset mappings).

Horse
A gene patch (fixing split genes) based on human/mouse 1:1 orthologues. Therefore we have a new gene set.

Human

  • cDNA update
  • New ensembl-vega merge delivering a “new gene set”.

Mouse

  • cDNA update
  • New ensembl-vega comparison, delivering a “new gene set” .

New gene sets (ncRNA genes) for several low coverage genomes:
Sloth (Choloepus hoffmanni), armadillo (Dasypus novemcinctus), kangaroo rat (Dipodomys ordii), elephant (Loxodonta africana), hyrax (Procavia capensis), megabat (Pteropus vampyrus), tarsier (Tarsius syrichta), dolphin (Tursiops truncatus) and alpaca (Vicugna pacos).

Mart

  • New functional genomics mart

Core
Minor schema changes

  • cDNA update
  • Update versions (patch_53_54_a.sql)
  • Increase size of oligo_probe.name (patch_53_54_b.sql)
  • Increase size of external_db.db_name (patch_53_54_c.sql)
  • Move analysis_id from identity_xref to object_xref (patch_53_54_d.sql)
  • Increase size of analysis.logic_name (patch_53_54_e.sql)


Variation and Functional Genomics

  • Schema change to source table to add description column for web display
  • Updated zebafish database
  • Import Illumina data whenever available
  • Recalculate consequence type for mouse regulatory feature
  • eFG array mapping: Human, Mouse, Rat, Drosophila
  • Affymetrix (UTR/IVT + ST), Illumina (WG)

New mouse DNAse data to support the first Mouse RegulatoryBuild

Code Other

  • Amazon EC2 public datasets updated
  • New GO database (ensembl_ontology_54) and API
  • Changing default behaviour of TranscriptAdaptor
  • Translation attribs modified
  • Remove entries with spaces from species.classification
  • Gene name and xref projections


Pairwise alignments

Update the pairwise alignments for zebrafish (Danio rerio):

  • human-zebrafish translated BLAT-NET
  • mouse-zebrafish translated BLAT-NET
  • rat-zebrafish translated BLAT-NET
  • chicken-zebrafish translated BLAT-NET
  • frog-zebrafish translated BLAT-NET
  • tetraodon-zebrafish translated BLAT-NET
  • fugu-zebrafish translated BLAT-NET
  • medaka-zebrafish translated BLAT-NET
  • stickleback-zebrafish translated BLAT-NET
  • Ciona savignyi-zebrafish translated BLAT-NET
  • Ciona intestinalis-zebrafish translated BLAT-NET

Add new alignments for medaka:

  • human-medaka BLASTZ-NET (imported from UCSC)
  • mouse-medaka BLASTZ-NET (imported from UCSC)


The following files will be available for download:

  • EMF dumps for GeneTrees
  • EMF dumps for EPO and PECAN multiple alignments
  • BED files for 31 way GERP constrained elements
  • BED files for 12 way GERP constrained elements

Homologies and families

  • 49-way GeneTrees and Homologies, with new/updated gene sets and assemblies.
  • Multiple Sequence Alignments with consistency-based MCoffee
  • Meta-aligner (mafftgins+muscle+kalign+probcons).
  • Pairwise gene-based dN/dS calculations for high coverage species pairs.
  • Updated MCL families including all Ensembl AS isoforms and latest UniProt Metazoa.
  • Multiple Sequence Alignments with MAFFT

In March, explore Ensembl in the following events:

1-3: Presentation at the EURATools Annual meeting in Barcelona
5,6: Browser workshop at the Department of Genetics in Cambridge, UK
10: Browser workshop in Leuven, Belgium
13: Browser workshop at the Faculty of Science, Montevideo, Uruguay
16-19: Ensembl Module in the Open Door Workshop, Montevideo, Uruguay
19: Demo at the Bioinformatics Course, National Genetics Reference Lab, Manchester, UK
20: Browser workshop at the Max Delbrück Center in Berlin, Germany
31: Browser workshop at King’s College, London, UK
31 March, 1 April : Demo and Browser Workshop at the IGC Oeiras, Portugal
2,3 April: Ensembl API workshop at the IGC, Oeiras, Portugal

Check out microorganisms at Ensembl genomes featured in the EBI ‘Sequence to Genes‘ Workshop, EBI, Hinxton, UK

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

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.

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.

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.

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.

Views:

  • 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]

Components:

  • 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"


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

Data

  • 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.

Other

Happy Holidays, and Happy New Year from Ensembl!

The new year will start with some workshops given by our Outreach team on how to use our new interface (and the data behind the scenes!). We hope you have had time to explore and learn the layout! Remember to send any questions to our helpdesk.

Upcoming workshops in January, 2009:

11 Jan Ensembl Demo at the PAG XVII conference, San Diego, CA, USA
13-14 Ensembl 2-day browser workshop at the Universidad de Chile, Santiago, Chile
15-16 Modules in the EBI Bioinformatics Roadshow, UCLA, USA
19-20 Modules in the EBI Bioinformatics Roadshow, City of Hope, USA
22-23 Modules in the EBI Bioinformatics Roadshow, UCSF, USA
24 Browser course in the Computational Biology Workshop, Sultan Qaboos University, Muscat, Oman
26 Browser course in the 9th BioSapiens European School of Bioinformatics, Brussels, Belgium

That’s all for now!

If you have clicked on the GeneTree link in Ensembl (for example, the gene tree for IL2), you may have noticed that we have a new way of displaying large GeneTrees. This time, if you have a large gene family with lots of genes that you want to look at, you won’t need to ask the Miami Dolphins to let you plug your laptop into their huge screen…


This new feature in EnsemblCompara is called collapsible subtrees and allows for more compact, summarized views of interesting gene families like PAX2/PAX5/PAX8:

http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000075891

If you check the legend at the bottom, you will see that “blue triangles” correspond to collapsed subtrees that have within-species paralogs of your gene. If you want to see all the within-species paralogs expanded, you can click on the option “View paralogs of current gene“. You can even set that as a default if you want in the “Configure this page” options.

Jalview is a great way to view protein alignments in the tree. And were is my Jalview link now? Click on any internal node (square) in the tree, and be able to visualize the alignment (or subalignment) with the new Jalview applet by clicking on the Jalview link. You have to have Java installed though, or the link won’t show. The two Jalview windows that pop up are one, the protein alignment and the other, the underlying TreeBeST tree. You can now use Jalview’s sorting feature to sort your sequences according to the tree with: Calculate->Sort->By Tree Order->URL. Having the tree associated to the alignment allows for a more phylo-centric visualization of sequence conservation: if you click at a point in the tree, a red vertical line will appear that divides the alignment into different groups. If you choose Colour->Percentage Identity, the shades of blue will be relative to the subgroups in your tree (e.g., fish versus placental mammals). This is also useful to spot segments in the alignment that don’t look that good, or gaps created in a subpart that can now be collapsed in the subalignment (Edit->Remove Empty Columns), or sequences that stand out as long branches in the alignment (View->Overview Window).


For even more tree funkiness, you can use PhyloWidget to visualize our NHX trees. Use our NHX tree (“Configure this page->Output for normal tree->NHX->Save and Close->Gene Tree(text)“) to copy+paste the representation of the GeneTree into Phylowidget, with duplication/speciation events (red/blue), bootstrap values (greyscale) and taxonomy levels “View->Rendering->Show clade labels“. Then use the “Zoom in/Zoom out” features, or clicking on an internal node, the “Tree Edit->collapse“, and specially the “View->Branch lenghts [x]” and the “View->Layout->Options->Branch Scaling” options.


We hope these new features will help you in your research. We have some new ideas that we are currently testing to visualize even more phylogenetic information, and help make better judgement on the orthology and paralogy relationships in our EnsemblCompara GeneTrees. Stay tuned for more updates!