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Bioinformatic_Databases and Sequence Analysis
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- 2. Some databases inthe 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 .................. !!!!
- 3. What we expectfrom 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
- 4. PRIMARY DATABASES Containsbio-molecular data in its original form. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Once given a database accession number, the data in primary databases are never changed. Examples :- GenBank, EMBL and DDBJ for DNA/RNA sequences, SWISS-PROT and PIR for protein sequences and PDB for molecular structures.
- 5. Biological Sequence Databases •Sequence databases • Structure databases
- 6. Nucleotide databases • InternationalNucleotide Sequence Database Collaboration (INSDC) – NCBI – EMBL – DDBJ
- 7. Standard contents ofa sequence database • Sequences • Accession number • References • Taxonomic data • Annotation/curation • Keywords • Cross-references • Documentation
- 8. Genbank • An annotatedcollection of all publicly available nucleotide and proteins • Set up in 1979 at the LANL (Los Alamos). • Maintained since 1992 NCBI (Bethesda).
- 9. NCBI • Very comprehensivebiological 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/
- 10. • 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.
- 11. Tools for analysis •BLAST • Primer-BLAST • ORF finder • Genome workbench
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- 14. Protein Sequence databases •UniProt • PFAM • Prosite • Motif scan
- 15. UniProt • Universal ProteinResource • Formed through the merger of : – SIB – EBI-SwissProt – TrEMBL – PIR
- 16. Uniprot features • Blast •Align • Retrieve • ID mapping
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- 18. • PDB –Protein Data Bank • CATH • SCOP – Structural Classification of Proteins
- 19. Protein DataBank (PDB) •Important in solving real problems in molecular biology • Protein Databank • PDB Established in 1972 at Brookhaven National Laboratory (BNL) • Sole international repository of macromolecular structure data • Moved to Research Collaboratory for Structural Bioinformatics http://www.rcsb.org/
- 20. PDB: example HEADER LYASE(OXO-ACID)01-OCT-91 12CA 12CA 2 COMPND CARBONIC ANHYDRASE /II (CARBONATE DEHYDRATASE) (/HCA II) 12CA 3 SOURCE HUMAN (HOMO SAPIENS) RECOMBINANT PROTEIN 12CA 5 AUTHOR S.K.NAIR,D.W.CHRISTIANSON 12CA 6 REVDAT 1 15-OCT-92 12CA 0 12CA 7 JRNL AUTH S.K.NAIR,T.L.CALDERONE,D.W.CHRISTIANSON,C.A.FIERKE 12CA 8 JRNL TITL ALTERING THE MOUTH OF A HYDROPHOBIC POCKET. 12CA 9 JRNL TITL 2 STRUCTURE AND KINETICS OF HUMAN CARBONIC ANHYDRASE 12CA 10 JRNL TITL 3 /II$ MUTANTS AT RESIDUE VAL-121 12CA 11 JRNL REF J.BIOL.CHEM. V. 266 17320 1991 12CA 12 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 071 12CA 13 REMARK 1 12CA 14EMARK 3 AUTHORS HENDRICKSON,KONNERT 12CA 20 REMARK 3 R VALUE 0.170 12CA 21 REMARK 3 RMSD BOND DISTANCES 0.011 ANGSTROMS 12CA 22 REMARK 3 RMSD BOND ANGLES 1.3 DEGREES 12CA 23 REMARK 4 12CA 24 REMARK 4 N-TERMINAL RESIDUES SER 2, HIS 3, HIS 4 AND C-TERMINAL 12CA 25 REMARK 4 RESIDUE LYS 260 WERE NOT LOCATED IN THE DENSITY MAPS AND, 12CA 26 REMARK 4 THEREFORE, NO COORDINATES ARE INCLUDED FOR THESE RESIDUES. 12CA 27 ………
- 21. wwPDB • Contains informationabout 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
- 22. • 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
- 23. CATH • Classification ofproteins based on domain structures • Each protein chopped into individual domains and assigned into homologous superfamilies. • Hierarchial domain classification of PDB entries.
- 24. 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
- 25. SCOP • Description ofstructural and evolutionary relationships between all the proteins with known structures • Uses the PDB entries • Search using keywords or PDB identifiers
- 26. Hierarchy in SCOP •Class • Fold • Superfamily • Family • Species
- 27. SECONDARY DATABASES Contains dataderived from the results of analysing primary data Manually created or automatically generated Contains more relevant and useful information structured to specific requirements Example :- PROSITE, PRINTS, BLOCKS, Pfam
- 28. Pfam • Proteins containconserved regions • Based on the conserved regions, proteins are classified into families • Provides links to external databases like PDB, SCOP, CATH etc.
- 29. Pfam: Features • Sequencesearch • View Pfam family • View a clan • View a sequence • View a structure • Keyword search
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- 32. COMPOSITE DATABASES Collectionof various primary database sequences Renders sequence searching highly efficient as it searches multiple resources Examples :- NRDB (Non Redundant Database), OWL, MIPSX, SWISS PROT + TrEMBL
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Editor's Notes
- #6 Each database exchange data every day. Each database has its own sequence submission and retrieval tools They follow a standardized annotation The Collaboration created a Feature Table Definition that outlines legal features and syntax
- #9 Currently, NCBI receives and processes about 20,000 direct submission sequences per month, in addition to the approximately 200,000 bulk submissions that are processed automatically. Collaboration with EMBL and DDBJ
- #10 Database continues to grow at exponential rate. Doubling in size every 10 months Has sequences of 250,000 distinct organisms
- #11 All tools can be downloaded and used on your local workstations as standalone.