Bioinformatic_Databases_2.ppt Bioinformatics

1. Biological Databases

2. 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 .................. !!!!

3. 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

4. Biological Databases
• Sequence databases
• Structure databases

5. Sequence databases
• Nucleotide databases
• Protein databases

6. Sequence databases

7. Nucleotide databases
• International Nucleotide Sequence
Database Collaboration (INSDC)
– NCBI
– EMBL
– DDBJ

8. Standard contents of a sequence
database
• Sequences
• Accession number
• References
• Taxonomic data
• Annotation/curation
• Keywords
• Cross-references
• Documentation

9. 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/

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

12. Protein Sequence databases
• UniProt
• PFAM
• Prosite
• Motif scan

13. UniProt
• Universal Protein Resource
• Formed through the merger of :
– SIB
– EBI-SwissProt
– TrEMBL
– PIR-PSD

14. • 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)

15. Uniprot features
• Blast
• Align
• Retrieve
• ID mapping

16. 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.

17. Pfam: Features
• Sequence search
• View Pfam family
• View a clan
• View a sequence
• View a structure
• Keyword search

18. 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

19. Gene Indices Software Tools
• TGI Clustering tools
• Clview
• SeqClean
• Cdbfasta/cdbyank

20. Structural databases

21. • PDB – Protein Data Bank
• CATH
• SCOP – Structural Classification of Proteins

22. 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

23. • 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

24. 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.

25. 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

26. SCOP
• Description of structural and evolutionary
relationships between all the proteins with
known structures
• Uses the PDB entries
• Search using keywords or PDB identifiers

27. Hierarchy in SCOP
• Class
• Fold
• Superfamily
• Family
• Species

28. Thank you