Biological Databases Pharmamatrix Workshop 2010 -Philip Winter -Ishwar V. Hosamani.
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Transcript of Biological Databases Pharmamatrix Workshop 2010 -Philip Winter -Ishwar V. Hosamani.
Some databases in the field of molecular biology…
AATDB, AceDb, ACUTS, ADB, AFDB, AGIS, AMSdb, ARR, AsDb,BBDB, BCGD,Beanref,Biolmage,
BioMagResBank, BIOMDB, BLOCKS, BovGBASE,BOVMAP, BSORF, BTKbase, CANSITE, CarbBank,CARBHYD, CATH, CAZY, CCDC, CD4OLbase, CGAP,
ChickGBASE, Colibri, COPE, CottonDB, CSNDB, CUTG,CyanoBase, dbCFC, dbEST, dbSTS, DDBJ, DGP, DictyDb,Picty_cDB, DIP, DOGS, DOMO, DPD, DPlnteract, ECDC,ECGC, EC02DBASE, EcoCyc, EcoGene, EMBL, EMD db,ENZYME, EPD, EpoDB, ESTHER, FlyBase, FlyView,GCRDB, GDB, GENATLAS, Genbank, GeneCards,
Genline, GenLink, GENOTK, GenProtEC, GIFTS,GPCRDB, GRAP, GRBase, gRNAsdb, GRR, GSDB,
HAEMB, HAMSTERS, HEART-2DPAGE, HEXAdb, HGMD,HIDB, HIDC, HlVdb, HotMolecBase, HOVERGEN, HPDB,HSC-2DPAGE, ICN, ICTVDB, IL2RGbase, IMGT, Kabat,
KDNA, KEGG, Klotho, LGIC, MAD, MaizeDb, MDB,Medline, Mendel, MEROPS, MGDB, MGI, MHCPEP5
Micado, MitoDat, MITOMAP, MJDB, MmtDB, Mol-R-Us,MPDB, MRR, MutBase, MycDB, NDB, NRSub, 0-lycBase,OMIA, OMIM, OPD, ORDB, OWL, PAHdb, PatBase, PDB,PDD, Pfam, PhosphoBase, PigBASE, PIR, PKR, PMD,
PPDB, PRESAGE, PRINTS, ProDom, Prolysis, PROSITE,PROTOMAP, RatMAP, RDP, REBASE, RGP, SBASE,
SCOP, SeqAnaiRef, SGD, SGP, SheepMap, Soybase,SPAD, SRNA db, SRPDB, STACK, StyGene,Sub2D,
SubtiList, SWISS-2DPAGE, SWISS-3DIMAGE, SWISS-MODEL Repository, SWISS-PROT, TelDB, TGN, tmRDB,TOPS, TRANSFAC, TRR, UniGene, URNADB, V BASE,VDRR, VectorDB, WDCM, WIT, WormPep, YEPD, YPD,
YPM, etc .................. !!!!
What we expect from a database..!!
• Sequence, functional, structural information, related bibliography
• Well Structured and Indexed• Well cross-referenced (with other databases)• Periodically updated• Tools for analysis and visualization
Nucleotide databases
• International Nucleotide Sequence Database Collaboration (INSDC)– NCBI– EMBL– DDBJ
Standard contents of a sequence database
• Sequences• Accession number• References• Taxonomic data• Annotation/curation• Keywords• Cross-references• Documentation
NCBI
• Very comprehensive biological database• GENBANK: The nucleotide sequence database• Provides 42 different resource• Provides a simple and easy to use web
interface
http://www.ncbi.nlm.nih.gov/
• Sequence submission: done using Bankit or Sequin
• Search Engine for data retrieval: Entrez• Retrieves information across all the resources
under NCBIExample: PubMed, taxonomy, SNP, PubChem etc.
UniProt
• Universal Protein Resource• Formed through the merger of :– SIB– EBI-SwissProt– TrEMBL– PIR-PSD
• Entry names are often the names of the gene followed by the species.
• Accession numbers are of the following format:
• e.g. P26367 (PAX6_HUMAN)
Pfam
• Proteins contain conserved regions• Based on the conserved regions, proteins are
classified into families• Provides links to external databases like PDB,
SCOP, CATH etc.
Pfam: Features
• Sequence search• View Pfam family• View a clan• View a sequence• View a structure• Keyword search
Gene Indices• Project aimed at indexing genes and their
variants in the various genome sequences.
• Creating a catalogue of genes in a wide range of organisms
• Reduce redundancy
wwPDB
• Contains information about experimentally determined structures of proteins, nucleic acids, and complex assemblies
• RCSB-PDB, PDBe, PDBj, BMRB – repositories of protein structure data
• Files in PDB, mmCIF, PDBML/XML formats
• Advanced search – provides comprehensive information about a protein.
• Sequence info, domain info, sequence similarity, literature, apart from the details of the structure.
• Cross referenced to SCOP and CATH
CATH
• Classification of proteins based on domain structures
• Each protein chopped into individual domains and assigned into homologous superfamilies.
• Hierarchial domain classification of PDB entries.
CATH hierarchy
• Class – derived from secondary structure content is assigned automatically• Architecture – describes gross orientation of secondary
structures, independent of connectivity• Topology – clusters structures according to their
topological connections and numbers of secondary structures• Homologous superfamily – this level groups
together protein domains which are thought to share a common ancestor and can therefore be described as homologous
SCOP
• Description of structural and evolutionary relationships between all the proteins with known structures
• Uses the PDB entries• Search using keywords or PDB identifiers