This document discusses databases in bioinformatics. It begins by noting the rapid increase in biological data from sources like gene sequences, protein sequences, structural data, and gene expression data. It then defines biological databases as structured, searchable collections of data that are periodically updated and cross-referenced. The major purposes of databases are to make biological data available, systematize the data, and allow analysis of computed biological data. The document provides a brief history of biological databases and sequencing efforts. It also classifies biological databases based on data type, maintenance status, data access, data sources, database design, and organism. Specific databases discussed include DDBJ, EMBL, GenBank, Swiss-Prot, and NCB

1. DATABASES IN
BIOINFORMATICS

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. 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. 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. …
 First genome published was of free
living virus haemophilus influenzae in
1995
 Genome?
 All genes ? Or all DNA?
 Why are complete genome
interesting?

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. 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. Classification scheme for
biological databases
Data type
Maintenance status
Data access
Data source
Database design
Organism

9. Data type
 Genome database
 Sequence database
 Structure database
 Microarray database
 Chemical database
 Pathway database
 Enzyme database
 Disease database
 Literature database

10. Based on maintenance status
NCBI EMBL SIB

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. Based on data sources
Based on
data
sources

13. Primary databases
 Contains original data from the
researchers
 Public or open access mostly
 NCBI , GENEBANK
 EMBL
 SWISS-PROT
 NDB

14. Secondary databases
 Results from entries of primary
database
 Manually created or automatically
generated
 Swiss-prot is an example of secondary
database

15. Thanks…

16. Biological
sequence
databases
Lecture # 5
By:
Hira Shahzad

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

21. 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

22. Good luck 