Ensembl 54

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

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