27 February, 2009

Ensembl 54

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


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).

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


  • cDNA update
  • New ensembl-vega merge delivering a "new gene set".
  • 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).

  • New functional genomics mart
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

17 February, 2009

Ensembl Workshops in March, 2009

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.