Ensembl Chicken What's New v31.1g (29 April 2005)

	Ensembl: Latest Developments
	v31.1g Update The Ensembl team are pleased to announce the release of version 31 of Ensembl. This release includes a new species, Ciona intestinalis, new assemblies for Honeybee and C. elegans, and a complete set of paralogue data for all Ensembl species. New data in v31 Multi-species Comparative genomics (ensembl_compara_31) Orthologues/Paralogues/Families Import paralogues data for all Ensembl species New orthology build New family build Whole Genome Alignments Fixed missing %id in Rat translated BLAT vs Tetraodon, Zebrafish and Chicken Fixed missing %id in Rat Blastz vs Human Rat Blastz vs Mouse Ciona translated BLAT vs Danio, Chicken and Human Honeybee translated BLAT vs Drosophila and Anopheles Gene Ontology (ensembl_go_31) The GO database has been updated with the April 2005 release from www.geneontology.org. Chicken (Gallus gallus) Variation Duplicate genotype data has been removed from the variation database, with the result that a few r2 values have changed. The chicken database version has been bumped to 1g, e.g. gallus_gallus_core_31_1g Schema changes in v31 Core database Gene table The 'type' column has been renamed to 'biotype' to give more indication of its contents. Allowed biotypes: protein-coding non-coding ncRNA Mt-rRNA Mt-tRNA snRNA-pseudogene snoRNA-pseudogene scRNA-pseudogene miRNA-pseudogene rRNA-pseudogene Mt-tRNA-pseudogene snoRNA miRNA snRNA rRNA misc_RNA-pseudogene tRNA-pseudogene scRNA misc_RNA pseudogene processed pseudogene unprocessed pseudogene immature antisense artifact transposon IG-segment IG-pseudogene-segment unclassified Added column 'confidence', of type enum( 'KNOWN', 'NOVEL', 'PREDICTED', 'PUTATIVE' ). We have found that known and novel in Ensembl mostly classify the evidence that was used to build the gene, so predicted and putative describe somewhat less-well-classified ( flaky or ab initio) evidence. Added column 'source' to denote the origin of a gene prediction, e.g. ensembl, vega, genoscope, flybase, wormbase, refseq, genewise. The 'gene_description' table has been removed, and the information moved to a new column 'description' in the 'gene' table. Although the gene description is similarly a piece of information that comes late in the process of the gene build as, for example, the stable id, it comes together with the display_xref and deserves a place in the gene table itself. Transcript table To better accommodate transcript-centric views on the genome, the transcript table now has similar columns: add transcript.biotype add transcript.confidence add transcript.description Regulatory regions Three new tables have been added in preparation for the release of regulatory region data. The tables, which are currently empty, are: regulatory_feature regulatory_feature_object regulatory_motif Variation Read_coverage table New table read_coverage, containing coordinates that correspond to genomic locations that are covered by 2 different reads. New features in v31 Apr2005 Archive The last release of Ensembl, v30, is still available at http://apr2005.archive.ensembl.org/ A table listing the assemblies present in the archives is available at: http://archive.ensembl.org/assembly.html For more information about Ensembl Archive sites see http://archive.ensembl.org/.