Ensembl Chicken What's New v24.1a.1 (1 September 2004)

	Ensembl: Latest Developments
	v24.1a.1 Update The new/updated Chicken data in release 24 are:  SNP database   New SNP database  Lite database   New database with the new SNP data  Compara database   New whole genome alignments for Danio, Mouse, Tetradon (as these are new assemblies).   New homology and family data Family rebuilt to incorporate new genomes (Honeybee, Danio, Mouse, Tetraodon). MUSCLE was used for the family multiple sequence alignments rather than ClustalW. Families 1, and 17 were unable to run with MUSCLE and were run with ClustalW. All others were run with MUSCLE. All families have multiple alignment CIGAR lines defined for their peptide members.   In-house production of BLASTZ - mouse vs human - mouse vs rat  (will be updated with UCSC data in october release) - mouse vs chicken  (will be updated with UCSC data in october release) - C. elegans vs C. briggsae   In-house production of translated BLAT mouse vs zebrafish mouse vs Fugu rubripes mouse vs Tetraodon nigroviridis mouse vs chicken zebrafish vs Fugu rubripes zebrafish vs Tetraodon nigroviridis zebrafish vs chicken zebrafish vs rat Tetraodon nigroviridis vs chicken, T. nigroviridis vs Fugu rubripes, T. nigroviridis vs human, T. nigroviridis vs rat Schema changes in v24  Core database   Added 'display_label' column to prediction_transcript.   Changed indices on align feature tables to improve performance of range queries.   SQL has been provided to enable schema 23 databases to be patched to schema 24 without the need to re-download the data.  Compara database   New tables: peptide_align_feature, analysis   Changed tables:   - added NOT NULL to dnafrag.dnafrag_type, sequence.length, and sequence.sequence (backwards compatible)   - homology: added column subtype varchar(40)   - homology_member : added column peptide_align_feature_id int(10) The homology.subtype is a more detailed classification of the nature of the homology. Changes are transparent to both MART and the web.   Extended Protein/Gene homology algorithm: Adapted for cases where there are equal 'best' hits (same query peptide hits multiple target peptides with same score, evalue, %identity, %positivity). Usually caused by target peptides having identical sequence.   Extended BRH labeling New homology description naming to correspond with algorithm changes. The old naming from schema 23 was BRH and RHS. BRH is now divided into 2 different naming categories:    1) UBRH - (Unique Best Reciprocal Hit) These are BRHs where there is only one uniquely best hit in both directions. Or a simple 1-to-1 BRH    2) MBRH - (Multiple Best Reciprocal Hit) These are BRHs where there were multiple but identical best hits in one or both directions. This can occur when there is perfect protein sequence duplication of translated genes within a species. In the old algorithm a random BRH was picked from the equally bests, now they are all reported. RHS - (Reciprocal Hit base on Synteny): unchanged from schema 23   New homology subtype For MBRH types there are the following subtypes defined:    1) MBRH , subtype ='DUP 1.#' (eg 1.3 or 1.5) These MBRHs are defined such that all the BRHs in the web of interconnection fall where there is only 1 gene in one species aligning equally best with # genes in the other species such that all these other genes fall on the same chromosome and within 1.5 megabases of each other. Hence these correspond to a highly probable recent 1-to-many gene duplication event and are paralogs. In the previous release one of these would have been a BRH and the rest would have been RHS.     2) MBRH, subtype = 'SYN' A homology of this subtype is one pair from a complex MBRH graphs which is syntenous (like an RHS) with a UBRH or an MBRH/DUP. In the previous release this may have been a BRH or a RHS    3) MBRH, subtype = 'complex' This is one pair from a complex MBRH graph that can't be easily classified. In the previous release this may have appeared as a BRH or may have been skipped. For descriptions/types UBRH and RHS there are no subtypes defined yet. New features in v24  SNPView   The SNP neighbourhood image now has a Features drop-down menu, similar to the menus on ContigView. This menu provides options for displaying all SNPs, just genotyped SNPs and different transcripts on the image.   The selected SNP is highlighted in the neighbourhood image.  Sitemap   Updated sitemap for www.ensembl.org  Drawing code   Code simplified to allow more tracks to be created without writing additional modules - by just using the drawing code configuration.   Configuration-only drawing code simplified by addition of "add_tracks" family of calls to the EnsEMBL::Web::UserConfig..  GeneView   Ab-initio predictions now shown on the transcript neighbourhood image.  API   Registry added: a central static hash for storage/retrieval for all the adaptors. Adaptor calls are backwards compatable and all old code should work exactly the same as previously but underlying code will now utilise the Registry. New methods allow easier access to adaptors via the Registry.  Mart   Mart has new attributes and filters around UniProt ids and UniProt accessions. This will allow users to filter on lists of UniProt ids or accessions regardless of their original source (UniProt/Swiss-Prot or UniProt/TrEMBL). Currently, the original UniProt/Swiss-Prot and UniProt/TrEMBL filters and attributes have also been retained.