Molecular Biology Databases - CNB - Protein Design Group

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PRIMARY BIOLOGICAL DATA SOURCES• Genome sequencing projects: genome sequences• Functional genomics: gene expression data• Proteomics: protein catalogues, postranslational modifications• Structural genomics: protein structures• Functional interactions between cellular components:gene regulatory networks• Physical interactions between proteins: protein interaction networks• Diverse experimental data: non structured information=>publications
GROWING NUMBER OF DATABASESThe number of molecular biology databases is also highly increasing• Because of huge data amount and new types of biological data (less)• Due to database specialization (most), e.g. by taxonomic group
Page 1 and 2: MOLECULAR BIOLOGYDATABASESJuan Carl
Page 3: Ouellette, 2000
Page 7 and 8: HOW TO ACCESS DATABASESDatabases ar
Page 9 and 10: CONTENT OF PRIMARY DATABASESExperim
Page 11 and 12: CLASSIFICATION OF MOLECULARBIOLOGY
Page 13 and 14: DATABASE SEARCHES:QUERY TYPESTEXT Q
Page 15 and 16: DATABASE SEARCHES:QUERY TYPESQUERIE
Page 17 and 18: NUCLEOTIDE DATABASESGenBank• Main
Page 19 and 20: GENOME DATABASESEnsemblEnsembl, EBI
Page 21 and 22: GENOME DATABASESEntrez Genome• In
Page 23 and 24: GENE-CENTERED DATABASESComplete inf
Page 25 and 26: PROTEIN DATABASESNon-redundant data
Page 27 and 28: PROTEIN DATABASESUniProtKB/Swiss-Pr
Page 29 and 30: STRUCTURE DATABASESProtein Data Ban
Page 31 and 32: PROTEIN DOMAINS DATABASESProtein do
Page 33 and 34: GENE EXPRESSION DATABASESGene expre
Page 35 and 36: PATHWAY DATABASESDisplay metabolic
Page 37 and 38: ONTOLOGIES IN MOLECULAR BIOLOGYCont
Page 39 and 40: GENE ONTOLOGYDeveloped and maintain
Page 41 and 42: GenBank and EMBL● GenBank and the
Page 43 and 44: • Entrez is the indexing and data
Page 45 and 46: MAIN DATABASESACCESIBLE WITH ENTREZ
Page 47: FASTA format> essentialGIAccession.
Page 50 and 51: GBFF: FEATURESFEATURESLocation/Qual
Page 52 and 53: EMBL AND SwissProt FORMATThe field
Page 54 and 55:
EMBL AND SwissProt FORMATFT source
Page 58 and 59:
• Sequence Retrieval System is a
Page 60:
ACKNOWLEDGMENTSThis presentation co
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