Ensembl Chicken What's New v22.1.1 (2 June 2004)

	Ensembl: Latest Developments
	v22.1.1 Release Ensembl 22 presents an annotation of the first draft chicken genome assembly. The chicken genome sequence was determined by whole genome shotgun at the Genome Sequencing Center at Washington University, St Louis. The analysis of the chicken sequence involves an international group of scientists including individuals from the US, UK, Europe and China. A slightly modified Ensembl gene build was run for chicken, resulting in 17784 genes with 185326 exons. Continuing analysis suggests that about 10% of the gene content of chicken is absent from this gene build. Around half of this missing content can be attributed to representation issues in the whole genome shotgun, probably due to high GC content regions not being well represented. The other half of the missing set is poorly represented as one or two exon assemblies (in particular in chromosome Un) which did not pass Ensembl's quality for gene structures. This QC level has been set to avoid spurious pseudogene structures being called as genes. We are working with our colleagues in the chicken community to analyse these data further and the analysis group expects to submit a paper this summer in addition to providing improved data resources. The new chicken data in release 22 are:   Core database   EST database   ESTgene database   Compara database - New homology analysis including chicken and honeybee - Orthologue analysis was extended so that now all species pairs have putative orthologues. For cross-phylum analyses (e.g. mosquito vs C.elegans), only BRH (best reciprocal hit) were calculated. - Protein families recalculated so to include the latest SWISSPROT and SPTREMBL Schema changes in v22  Core database   2 new tables (translation_attrib & transcript_attrib) added, for handling exceptional cases in transcripts/translations, e.g selenocysteins and RNA edits. Data to populate these tables is still in preparation.   The "code" column in the "misc_set" table was expanded from varchar(15) to varchar(25).  SNP database   "hapmap_snp" column added to the "RefSNP" table to provide a boolean flag indicating whether this RefSNP has been typed in the HapMap project or not.  Compara database   added column "chr_strand" to "member" table which copies Gene and Transcript strandedness (1 or -1) from the core databases   added column "locator" to "genome_db" table which stores a locator string which describes how to get a DBAdaptor for the corresponding core database. It is used in pipeline production, but set to an empty string for release. New features in v22  MultiContigView   We are pleased to announce a new comparative genomics view for Ensembl: MultiContigView. This page displays simultaneous contigviews for multiple species, aligned by compara genomic alignment blocks. e.g. MultiContigView.   You can enter the page on a location (from one species), along with the name of one or more additional species. The initial alignment is selected as the best available between the two species, interpolated from the DNA align features in the compara database. MultiContigView is linked to from ContigView (via Compara DNA align features), and GeneView.   This is the initial release of this page, and we are planning a number of improvements. We would be appreciative of any feedback you might have, good or bad, about this display.  SNPView   Now displays a link to the HapMap Project if the SNP has been typed in HapMap.  Site Maps   The site maps have been reworked, and are now generated dynamically from the available data. This means they are more up-to-date, more accurate, and more useful for navigating the site. [more].  ContigView   Affy probe track added. The Affymetrix probe hits stored in the core database are now displayed as a track on ContigView. This track can be switched on and off from the 'Features' menu.   Transcript tracks are now collapsible. Transcript tracks can be collapsed down into genes by clicking the red "-" symbol to the left of the track name.