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Development of Bioinformatics and its application on Biotechnology

Explore the development of bioinformatics and its impact on biotechnology, including databases, algorithms, protein modeling, and personalized medicine advancements. Learn about key resources and tools in molecular biology analysis.

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Development of Bioinformatics and its application on Biotechnology

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

  2. What is Bioinformatics? (1) Bioinformatics -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 http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

  8. 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 http://www.ebi.ac.uk/embl/

  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) http://www.ebi.ac.uk/swissprot/

  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 http://www.biochem.ucl.ac.uk/bsm/dbbrowser/protocol/ecenzfrm.html

  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 http://www.rcsb.org/pdb/

  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)

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

  16. 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 http://www.bioinformaticssolutions.com/products/prospect.php

  17. Example of 3D-Protein Model

  18. 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

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

  20. 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

  21. Website for BLAST http://www.ncbi.nlm.nih.gov/BLAST/

  22. 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

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

  24. 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

  25. 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

  26. 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

  27. Deinococcus radiodurans

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

  29. Evolutionary studies 2

  30. 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

  31. 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

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