1. Development of Bioinformatics and its application on Biotechnology
By Wong Tak Hong

2. What is Bioinformatics? (1)
-use of computer to store, analysis and manipulate biological information

3. What is Bioinformatics? (2)
-manage and manipulate sequence data
-use that sequence data in the analyses of gene, protein, and DNA function
-designing novel and incisive algorithms
-create new/maintain existing databases of information
-allowing open access to the records held within them

4. Onset of Bioinformatics
-Huge advances in the fields of molecular biology and genomics especially after Human Genome Project
-This cause massive amount of biological information available

5. Onset of Bioinformatics 2

6. What is developed?
-Biological databases are consistent data that are stored in a uniform and efficient manner
-These databases contain data from a broad spectrum of molecular biology area
-Primary databases contain
-information and annotation of DNA protein sequences
-DNA and protein structures and DNA and protein expression profiles
                                     

7. Genbank
-First database setup to store DNA sequence data, set up In 1982
-manage by National Centre Biotechnology Information
-currently holds about 17 billion bases from more than 100,000 organisms
-Each of the sequences are given an ID number for easy identification in the database

8. -a comprehensive database of DNA and RNA sequences
EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database
-a comprehensive database of DNA and RNA sequences
-manage by European Bioinformatics Institute (EBI)
-information collected from the scientific literature and patent applications
-supported by 17 countries in Western Europe
-currently contains nearly more than 10 million bases

9. SwissProt: -a database of protein sequence, function and structure
-manage by European Bioinformatics Institute
-provides a high level of integration with other databases
-a very low level of redundancy (means less identical sequences are present in the database)
                                     

10. EC-ENZYME:
The 'ENZYME' data bank contains the following data for a characterized enzyme:
-EC number
-Recommended name and Alternative names
-Catalytic activity
-Cofactors
-Pointers to the SWISS-PROT entry that correspond to the enzyme
-diseases associated with a deficiency of the enzyme

11. Website of EC-enzyme

12. Protein Data Bank
-manage by Research Collaboratory for Structural Bioinformatics (RCSB)
-a collection of all publicly available 3D structures of proteins, nucleic acids, carbohydrates
-variety of other complexes experimentally determined by X-ray crystallography and NMR

13. How rapidly developed?

14. Structural Analysis
-DNA sequences that encode proteins with specific function
-Researchers predict the 3D structure using protein or molecular modeling
-Experimentally determined protein structures (templates) are used
-to predict the structure of another protein that has a similar amino acid sequence (target)

16. Algorithm
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

17. PROSPECT -Protein Structure Prediction and Evaluation Computer Toolkit
-a protein-structure prediction system
-It construct a 3-D model of proteins
by protein threading
- Protein threading
Algorithms for protein fold recognition

18. Example of 3D-Protein Model

20. Advantages in Protein Modeling
-Examining a protein in 3D allows for greater understanding of protein functions
-providing a visual understanding that cannot always be conveyed through still photographs or descriptions

21. Homology and Similarity Tools
-Homology and Similarity Tools are use to analyses similarity between two sequence or structure
-the degree of similarity between two sequences can be measured
-applied in evolutionary studies

22. BLAST (Basic Local Alignment Search Tool)
-homology and similarity tools
-develop by NCBI
-Search programs designed for the Windows platform
-used to perform fast similarity searches for protein or DNA
-users can retrieve results and format their results in different format

23. Website for BLAST

24. Molecular Medicine
-Most of the disease has a genetic component and environmental component
-we can search for the genes directly associated with different diseases
-begin to understand the molecular basis of these diseases more clearly
-better treatments, cures and even preventative tests to be developed

25. Phenylketonuria (PKU)
The PAH
(phenylalanine hydroxylase)
gene maps
on chromosome 12
PAH

26. Personalized Medicine
-Development of the field of pharmacogenomics
-study of how an individual's genetic inheritance affects the body's response to drugs
-At present, doctors have to use trial and error to find the best drug to treat a particular patient
-In the future, doctors will be able to analyze a patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning

27. Microbial genomic application
-MGP (Microbial Genome Project) to sequence genomes of bacteria
-useful in energy production, industrial processing and toxic waste reduction
-scientists can begin to understand these microbes at a very fundamental level
-isolate the genes that give them their unique abilities to survive under extreme conditions

28. Waste clean up
-Deinococcus radiodurans is known as the world's toughest bacteria
-the most radiation resistant organism known
-Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals

29. Deinococcus radiodurans

30. Evolutionary studies -sequencing of genomes from different organism
-evolutionary studies can be performed to determine the tree of life
-find last universal common ancestor

31. Evolutionary studies 2

32. Impact of Bioinformatics 1
-Bioinformatics leads to advances in understanding basic biological processes, treatment, and prevention of many genetic diseases
-Bioinformatics has transformed the discipline of biology from a purely lab-based science to an information science as well

33. Impact of Bioinformatics 2
-modern biology and related sciences are increasingly becoming dependent on Bioinformatics
-Thus, Bioinformatics exhibits great potential in the future development of science and technology