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
- 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
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