Ensembl Fruitfly What's New v19.3a.1 (16 December 2003)

	Ensembl: Latest Developments
	New data in v19.3a.1    v19.3a.1 Update Ensembl Fruitfly release 19.3a.1 is a minor data/schema update, made to accompany the Human 34a and Rat 3a releases. The new Fruitfly data are   Updated Compara database Schema changes in v19    Compara Addition of two columns, "dn" and "ds" in the homology table These columns are filled only for some paired species, i.e. human/mouse, human/rat, mouse/rat and elegans/briggsae. For the other paired species, the ds values obtained were saturated and were viewed as unreliable. For those cases, the ds and dn columns are null. New Features in v19.3a.1    GeneDAS This release sees a further extension and incorporation of the DAS protocol into Ensembl. For a long time DAS has been used to include external annotations, including user's own data, on ContigView displays. This concept has now been applied to the GeneView display, enabling external annotations on specific genes to be incorporated into the page. The first dataset to be included is SwissProt literature references for genes. [ e.g. ] This is only the beginning for GeneDAS, and we are working on providing a number of data sources, as well as enabling users to display their own gene annotations.    GeneSNPView GeneSNPView is a new gene-centric SNP display. This page, linked from GeneView, shows details of SNPs and Pfam domains in, or close to, the exons of the transcripts of a particular gene. The SNP data includes their location, alleles, classification, and effects on the different transcripts. [ e.g. ]    ChromoView A new "tool" page has been added this release. ChromoView enables the customisable display of feature frequency data against a single chromosome or a karyotype. The data can be provided by cut-and-paste, by file upload, or by providing a URL of a datafile. ChromoView accepts a variety of formats, including simple tab- or space-delimited, PSL, BED and GFF. ChromoView is available for all species with an assembly mapped to chromosomes. [ e.g. ] Please let us know if you find ChromoView useful, or have suggestions for improvements.    GeneView Orthologues GeneView now displays further details from the Compara database. Orthologue predictions show how they were selected (Best Reciprocal Hit or Reciprocal Hit based on Synteny around BRH) and give a value for dN/dS where available.    ContigView tracks   New Anopheles Gap track (Decorations menu, Gaps). This track displays the location of gaps both between and within scaffolds.   Ensembl & Vega transcript tracks now show include the type of transcript in the labels below each transcript. This can be switched off by selecting "Concise labels" in the Decorations menu.   The BLAST hit track now shows additional match details.    Webcode redesign Release 19 sees the continued rollout of the redesigned webcode. Updated pages in this release are FASTAView, ExonView, MapView, AnchorView and SNPView.    MartView updates   Number of transcripts per gene is available for export and filtering.   Exons are flagged as constitutive or alternative depending on their presence or not in all the transcripts of a gene.   New data available on orthologous gene relationships See the EnsMart homepage for more details of Mart updates.