Ensembl Fruitfly What's New v25.3b.1 (1 October 2004)

	Ensembl: Latest Developments
	v25.3b.1 Update The main data updates in this release are in the Compara database, which has both new data and some schema changes.  New Data There are no new assemblies in Ensembl v 25.  Comparative genomics (ensembl_compara_25_1)   BLASTZ - Mouse/Rat BLASTZ_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in house). - Mouse/Chicken BLASTZ_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in house). - C.elegans/C.briggsae BLASTZ_GROUP_TIGHT now in - Tetraodon/Fugu BLASTZ_GROUP_TIGHT now in  Synteny - Mouse/Rat Synteny added - New synteny for Mouse/Chicken   Data bugs fixed: - Some cigar_line inversions have been corrected - Added N, S, dN, dS, LnL, threshold_on_ds values to the human paralogues  Mart database (ensembl_mart_25_1) - New build - Can now filter on Uniprot ID lists and Uniprot Accession lists, as well as SWProt and SPTrembl. These ID/accessions are also available as attributes. Schema changes in v25 Core database Tables gene_stable_id, exon_stable_id, transcript_stable_id & translation_stable_id - "created_date" and "modified_date" columns added (back). Both have been set to '2004-09-20 00:00:00'. Compara database These new changes were introduced - to enable whole genome multiple alignments storage/querying - to improve the method_link_species_set data (formely in method_link_species) consistency with the data actually present in compara Schema patch SQL has been provided to enable schema 24 databases to be patched to schema 25 without the need to re-download the data. Deleted Tables 'source' 'method_link_species' (replaced by the new 'method_link_species_set' table) New tables: 'method_link_species_set' 'genomic_align' 'genomic_align_group' Modified tables: - 'genomic_align_block' has lost some data now transfered to new tables 'genomic_align' and 'genomic_align_group' - 'member' has now 'source_name' instead of 'source_id' - 'family' has now 'method_link_species_set_id' instead of 'source_id' - 'homology' has now 'method_link_species_set_id' instead of 'source_id' Full details of the Compara schema and these changes can be found in CVS in ensembl-compara/docs/schema_doc.html