Ensembl Mosquito What's New v26.2b.1 (1 November 2004)

	Ensembl: Latest Developments
	v26.2b.1 Update  New Data This release includes a new human assembly and gene build in addition to fixes/updates in other species.  Comparative genomics (ensembl_compara_26_1)   Human/Chimp BLAST_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in-house)   Human/Mouse BLASTZ_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in-house)   Human/Rat BLAST_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in-house)   Human/Chicken BLAST_NET from UCSC (as well as BLASTZ_NET_TIGHT generated in-house)   Human/fugu TRANSLATED_BLAT   Human/tetraodon TRANSLATED_BLAT   Human/chicken TRANSLATED_BLAT   Human/Zebrafish TRANSLATED_BLAT   New synteny for Human/Chimp, Human/Mouse, Human/Rat, Human/Chicken   Orthologues rebuilt   Human paralogues rebuilt   Protein clusters rebuilt. Multiple alignments run with MUSCLE on each family, except family ENSF00000000041 that has been run with CLUSTALW.  Mart database (ensembl_mart_26_1)   New build Schema changes in v26 Core database Probeset data has been moved from the misc_feature_table to three new tables. This both extends the data associated with probes, and greatly improves retrieval speed for other misc_features. 3 new tables: affy_feature, affy_probe, affy_array - external_db table: db_name is now varchar(27) - density_feature: added a index on seq_region_id Schema patch SQL has been provided to enable schema 25 databases to be patched to schema 26 without the need to re-download the data. The 25 to 26 patch file is also available in CVS at ensembl/sql/patch_25_26.sql. The ensembl/sql/transfer_misc_affy.pl script can be used to move the affy data from misc_feature table to the new tables. Compara database Modified tables: - synteny_region table: new column 'method_link_species_set_id' - dnafrag_region table: 2 columns renamed from seq_start, seq_end to dnafrag_start and dnafrag_end respectively. - When possible primary keys are now UNSIGNED - genomic_align_block_id changed to UNSIGNED BIGINT in genomic_align and genomic_align_block tables - genomic_align_id changed to UNSIGNED BIGINT in genomic_align and genomic_align_group tables - perc_id changed to UNSIGNED TINYINT in genomic_align_block table - level_id changed to UNSIGNED TINYINT in genomic_align table In ensembl-compara/sql/table.sql all foreign-key constraints are now explicitly defined (even though MySQL ignores them). Full details of the Compara schema and these changes can be found in CVS in ensembl-compara/docs/schema_doc.html New features in v26  ExportView   A new tab, "Pip", has been added. This exports a sequence and annotation file for use in comparative sequence analysis tools like PipMaker, Vista or zPicture.  FeatureView   FeatureView displays the location of all alignments of the selected feature against the genome. Currently the display works for probe sets, DNA and protein sequences. You can get to FeatureView from the alignment tracks in ContigView, from TextView and from the Affymetrix probes in GeneView.