Ensembl Compara - CNB - Protein Design Group

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Ensembl: What do you get?Jul 2007Genome Annotation– Protein coding gene structureConsistent with genome, predicted across all vertebratesManual annotations (human, mouse, zebrafish, MHC)– RNA genes (including miRNA)• Consistent with genome, predicted in across mammalsAdditional identifiers per genesAffymetrix, EntrezGene, Uniprot…• Comparative & Functional GenomicsGenome alignmentsBlastz, Blat, coordinated with UCSC– Homologues between genomes– Protein treesVariants (SNPs), strains, genotypesTiling array data• Infrastructure– Website, Data mining tool, database and data dump– Portable, extendable, open source system with database, API, website,pipeline
Ensembl groupsJul 2007GeneBuilders: sequence masking, gene buildingCore: database schema, stable id mappingCompara: protein homology, genomic sequencealignmentsFunctional Genomics: SNPs, probe mapping,functional dataMart: martification of the previous data for dataminingWeb: web site, new views for new dataUser support: help, workshops, tutorialsMore people: Research, DAS, VectorBase, Zebrafish,Systems...
Page 5: Timeline 2 : Genomes9/01 Release wi
Page 9 and 10: BilateriaNCBI Taxonomy for the 31sp
Page 11 and 12: Ensembl ComparaA single database wh
Page 13 and 14: Genomic AlignmentsBlastZNetused t
Page 15 and 16: Pecana consistency based multiple
Page 17 and 18: Encode ComparisonSPECIFICITYCOVERAG
Page 19 and 20: How to align suchlarge segments?New
Page 21 and 22: EnredoSolving the graphJul 2007Comm
Page 23 and 24: ORTHEUSBranch Transducer ModelFour
Page 25 and 26: HomologyBRH/RHS pairs of speci
Page 27 and 28: Load Genes and LongestTranslation f
Page 29 and 30: Protein trees and homologyDuplicati
Page 31 and 32: Gene tree : 1st data assessmentGood
Page 33: Jul 2007

Ensembl Compara - CNB - Protein Design Group

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