Ensembl Anopheles What's New v29.2d (21 February 2005)

	Ensembl: Latest Developments
	v29.2d Update The Ensembl team are pleased to announce the release of version 29 of Ensembl. This release includes the Consensus CDS (CCDS) transcript set in human, import of the Saccharomyces cerevisiae genome, an update of all variation databases to dbSNP 124, and a new genebuild for chimpanzee. New data in v29 Multi-species As the Ensembl versioning has changed slightly (the version number now increments with each release rather than with schema changes), the version suffix on the multi-species databases is now unnecessary. For example, the Compara database is now named ensembl_compara_29 rather than ensembl_compara_29_1. Comparative genomics (ensembl_compara_29) New family and putative orthologues sets due to modified mouse and chimp genesets and the addition of Saccharomyces cerevisiae to Ensembl. The same human, mouse and rat paralogues as last month. The following WGA have been removed from Ensembl to decrease the size of compara. Homo Canis BLASTZ_NET_TIGHT Homo Gallus BLASTZ_NET_TIGHT Mus Canis BLASTZ_NET_TIGHT Mus Fugu TRANSLATED_BLAT Mus Gallus BLASTZ_NET_TIGHT Rattus Fugu TRANSLATED_BLAT Rattus Gallus BLASTZ_GROUP Rattus Gallus BLASTZ_GROUP_TIGHT Rattus Xenopus TRANSLATED_BLAT Canis Xenopus TRANSLATED_BLAT Gallus Canis TRANSLATED_BLAT Danio Canis TRANSLATED_BLAT Tetraodon Canis TRANSLATED_BLAT Fugu Canis TRANSLATED_BLAT Fugu Gallus TRANSLATED_BLAT Fugu Tetraodon TRANSLATED_BLAT Fugu Xenopus TRANSLATED_BLAT And the remaining translated BLATs have been refiltered using more stringent parameters to try and decrease the size of compara. Mart databases: Owing to operational problems running the BioMart codebase (released last month) as part of Ensembl, Mart has temporarily been reverted to EnsMart. Mosquito (Anopheles gambiae) Variation  Updated to dbSNP 124 The mosquito database version has been bumped to 2d, i.e.anopheles_gambiae_core_29_2d Schema changes in v29 Core database peptide_align_feature table has had an increase in max_rows Schema patch The 28 to 29 patch file is available in CVS at ensembl/sql/patch_28_29.sql to enable schema 28 databases to be patched to schema 29 without the need to re-download the data. New features in v29 DAS Release v29 sees an overhaul of the Ensembl DAS systems. The different "types" of DAS - GeneDAS, ProteinDAS and standard sequence DAS - have been reconciled into a common system with a common configuration interface. This means that all of the Ensembl pages which display DAS sources (e.g. geneview, protview, contigview) can display all types of DAS source, and they can be configured with the same interface. KaryoView / Chromoview KaryoView now incorporates all the functionality of ChromoView, which has been removed. KaryoView can now display your own data on a karyotype or single chromosome, both as locations and as density plots. Feb2005 Archive The last release of Ensembl, v28, is still available at http://feb2005.archive.ensembl.org/ For more information about Ensembl Archive see http://archive.ensembl.org. FamilyView FamilyView has been redesigned using the updated webcode. The information is more clearly presented in a style consistent with the other pages in Ensembl. For an example page see here. LDView The new LDView page can now display r2 and D' LD values and plots centred around a gene, as well as around a SNP. A new link has been added to LDView from GeneView to simplify the investigation of LD around a gene of interest.