Molecular Biology Databases - CNB - Protein Design Group

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DATABASE SEARCHES:QUERY TYPESQUERIES by CONTENTThis type of fixedform query refers to searches performed against theCONTENT or CORE DATA, which, almost by definition, consists in abstractrepresentations:● Strings of characters that represent nucleotide or protein sequences.● Tables of atomic coordinates that represent three dimensional objects● Bitmap files that represent 2D gel images.
DATABASE SEARCHES:QUERY TYPESQUERIES by CONTENTFor example, in the case of a sequence database, we may be asking:Does a sequence exactly like:LLLIHRLHor similar to it, exists in the database?Because biological sequences change along time, or between individuals,this type of search is not a matter of finding exact matches in strings ofcharacters. On the contrary, it must consider the principles of molecularevolution.A number of algorithms have been developed to cope with that task, andBLAST is the most popular.
Page 1 and 2: MOLECULAR BIOLOGYDATABASESJuan Carl
Page 3 and 4: Ouellette, 2000
Page 5 and 6: GROWING NUMBER OF DATABASESThe numb
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: DATABASE SEARCHES:QUERY TYPESTEXT Q
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

Molecular Biology Databases - CNB - Protein Design Group

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