Loading in 2 Seconds...
Loading in 2 Seconds...
Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.
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
Biological Databases • Sequence databases • Structure databases
Nucleotide databases • Protein databases Sequence databases
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 NCBI Example: PubMed, taxonomy, SNP, PubChem etc.
Tools for analysis • BLAST • Primer-BLAST • B-Link • ORF finder • Genome workbench
Protein Sequence databases • UniProt • PFAM • Gene Index project
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)
Uniprot features Blast Align Retrieve ID mapping
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
Gene Indices Software Tools • TGI Clustering tools • Clview • SeqClean • Cdbfasta/cdbyank
PDB – Protein Data Bank • CATH • SCOP – Structural Classification of Proteins
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
Hierarchy in SCOP • Class • Fold • Superfamily • Family • Species