Molecular Biology Databases - CNB - Protein Design Group

More documents

Recommendations

Info

CONTENT OF SECONDARY DATABASESPredictions or interpretations based on information contained inprimary databases• Protein sequences, deduced from nucleotide sequences• Alignments of protein or nucleic acid sequences• Protein families, inferred by sequence similarity or by the presence ofcommon motifs or domains• Protein families, inferred by structural similarity• Reconstructed (predicted) cellular processes, such as metabolic pathways
CLASSIFICATION OF MOLECULARBIOLOGY DATABASESSecond classification scheme:Follows the well known layout to describe the levels of organization ofprotein structures.● Primary DBs: the content consists of SEQUENCES (primarystructure of nucleic acids or proteins).● Secondary DBs: the content consists of PATTERNS (regions oflocal regularity, for example, conserved motifs or domains).● Structure DBs: the content consists of sets of ATOMICCOORDINATES (three-dimensional packing of secondary structureelements).This scheme applies only to biological molecules (for example, a databaseof results from micro-array expression experiments would not fit).
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: CONTENT OF PRIMARY DATABASESExperim
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
show all

Molecular Biology Databases - CNB - Protein Design Group

Create successful ePaper yourself

Delete template?

Save as template?