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