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databases in bioinformatics

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databases in bioinformatics

  1. 1. DATABASES IN BIOINFORMATICS
  2. 2. Introduction  Fast increase in biological information  Biological science has now turned into a data rich science  Gene sequences  Amino acid sequences in proteins  Motifs and domains in proteins  Structural data from XRD & NMR  Metabolic pathways  Protein-protein interactions  Gene expression data DNA microarrays
  3. 3. Biological databases  Biological database is a collection of data which is structured, searchable, updated periodically and also cross- referenced.  Some databases are multi functional  Major purposes of databases is as follows:Availability of biological data Systemization of data Analysis of computed biological data
  4. 4. History  1956; first sequence database when insulin was sequenced  51 amino acids  Atlas of protein sequences and structures in 1965 by Margaret Day Hoff et al was a printed book.  Became base for PIR protein information resource  First nucleotide sequence: yeast tRNA  77 bases  During this time 3D structure of proteins was being studied and renowned PDB was made.
  5. 5. …  First genome published was of free living virus haemophilus influenzae in 1995  Genome?  All genes ? Or all DNA?  Why are complete genome interesting?
  6. 6. Aspects of genome analysis Ab initio Gene prediction Locus Gene identification by EST (expressed sequence tags) Gene prediction via EST Gene prediction via comparison, coding and regulatory regions
  7. 7. Features of biological databases 1) Data heterogeneity 2) High volume data 3) Uncertainty 4) Data Curation 5) Large scale data integration 6) Data sharing 7) Dynamic and subject to change
  8. 8. Classification scheme for biological databases Data type Maintenance status Data access Data source Database design Organism
  9. 9. Data type  Genome database  Sequence database  Structure database  Microarray database  Chemical database  Pathway database  Enzyme database  Disease database  Literature database
  10. 10. Based on maintenance status NCBI EMBL SIB
  11. 11. Based on data access 1) Publicly available 2) Available with copy wright 3) Browsing only, accessible but not downloadable 4) Academic but not freely available 5) Proprietary commercial 6) Restricted
  12. 12. Based on data sources Based on data sources
  13. 13. Primary databases  Contains original data from the researchers  Public or open access mostly  NCBI , GENEBANK  EMBL  SWISS-PROT  NDB
  14. 14. Secondary databases  Results from entries of primary database  Manually created or automatically generated  Swiss-prot is an example of secondary database
  15. 15. Thanks…
  16. 16. Biological sequence databases Lecture # 5 By: Hira Shahzad
  17. 17. DDBJ  DNA databank of japan  Nucleotide sequence database  Established in 1986  Has been working in collaboration with EMBL & NCBI  After 20 years another collaborative project named INSDC was formed EMBL Genebank DDBJ
  18. 18. SWISS-PROT  Protein sequence database  Maintained by SIB Swiss institute of bioinformatics in Switzerland and also the European bioinformatics institute EBI  The output format is swiss-prot file  That has been explained in molecular file formats
  19. 19. Good luck 

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