1. Bioinformatics and it’s methods Prepared by: Petro Rogutskyi E-mail: 187371@student.pwr.wroc.pl

2. Contents What is bioinformatics ? Current research in bioinformatics Genomics: DNA sequencing The Human Genome Project Proteomics: Protein Structure prediction Comparative modeling Interesting facts Conclusions Reference list 2

3. What is bioinformatics? (1) Bioinformatics is a science that involves close relation between biology and computers that influence each other and synergistically merging more than once. The data is usually collected from DNA, RNA, protein sequences 3

4. What is bioinformatics? (2) Bioinformatics techniques have been developed to identify and analyze various components of cells, such as gene and protein function, interactions and methabolic* and regulatory pathways. *Metabolism - is the set of chemical reactions that happen in living organisms to maintain life 4

5. Current Research in bioinformatics(1) Genomics* sequencing and comparative study of genomes to identify gene and genome functionality Proteomics – identification and characterization of protein related properties *Genome is the entirety of an organism's hereditary information. It is encoded in DNA 5

6. Current Research in bioinformatics(2) Cell visualization and simulation to study cell behavior Application to the development of drugs and anti-microbial agents 6

7. Genomics(1) Genomics is the study of the collective genetic material in an organism. This scientific discipline is focused on sequencing the DNA in an organism to form a complete picture, and then identifying specific genes in that sequence which could be of interest. 7

8. Genomics(2) In genomics, scientists analyze the DNA in every chromosome of the organism of interest. When a completely sequenced set of DNA has been created, this set is collectively known as a “genome.” The purpose of it is to define the function of each gene in genome 8

9. DNA Sequencing(1) The raw data for the genomic analysis are the DNA Sequences Sequencing simply means determining the exact order of the bases in a strand of DNA. Because bases exist as pairs, and the identity of one of the bases in the pair determines the other member of the pair, researchers do not have to report both bases of the pair. 9

10. DNA Sequencing(2) 10

11. Chain-Termination Method(1) Is the Most common method of DNA Sequencing, used today. This method is based on the principle that single-stranded DNA molecules that differ in length by just a single nucleotide can be separated from one another using a technique called polyacrylamide gel electrophoresis. 11

12. Chain-Termination Method(2) A DNA template A primer tagged with a mildly radioactive molecule or a light-emitting chemical DNA polymerase, an enzyme that drives the synthesis of DNA Four deoxynucleotides (G, A, C, and T) One dideoxynucleotide, either ddG, ddA, ddC, or ddT 12

13. Chain-Termination Method(3) 13

14. The Human Genome Project(1) The Human Genome Project, produced a very high-quality version of the human genome sequence that is freely available in the internet: http://www.ncbi.nlm.nih.gov/genbank/. http://www.ncbi.nlm.nih.gov/genbank/ The Sequence is derived from a some different person’s genomes 14

15. The Human Genome Project(2) The Human Genome Project was designed to generate a resource that could be used for a broad range of biomedical studies. More research can then be done to fully understand how the genome functions and to discover the genetic basis for health and disease. 15

16. Proteomics : Protein structure prediction(1) Genomic projects have provided large number of sequence information We Should obtain some benefit from this information. 16

17. Proteomics : Protein structure prediction(2) Understanding the structural basis for protein function enables rapid progress in systems biology that aims at identifying functional networks of proteins at a large scale from genomics and proteomics projects Rational drug design heavily relies on the structural knowledge of a protein 17

18. Proteomics : Protein structure prediction(3) A higher-level structure prediction is to model the three-dimensional structure of the protein or fold Structure of proteins can be modeled using comparative modeling 18

19. Comparative modeling Comparative modeling involves identifying a structural parent to an unknown sequence and the use of geometric constraints derived from the known structure to model the unknown sequence 19

20. Software used for comparative modeling(1) MODELLER uses an automated approach to comparative modeling. COMPOSER automatically constructs protein models using constraints derived from structurally conserved regions (SCRs). 20

21. Software used for comparative modeling(2) MPACK (Modeling Package) is an integrated protein-modeling suite designed to handle modeling of proteins effectively And even Web-based services: ESyPred3D (http://www.fundp.ac.be/urbm/bioinfo/e sypred/) That uses neural network to improve sequence alignment. Final model is obtained using MODELLERhttp://www.fundp.ac.be/urbm/bioinfo/e sypred/ 21

22. The results of modeling 22

23. Interesting Facts(1) The Chinese scientists from Hong-Kong University discovered that in 1 gram of bacteria we can encode 900 Terabytes of information 23

24. Interesting Facts(2) 24

25. Interesting Facts(3) Then scientists synthesize the DNA with needed sequence end insert it into the bacteria cells 25

26. Interesting Facts(4) Scientists of South Korea developed cats, that shine under ultra-violet with red color 26

27. Interesting facts(5) Bacteria successful in cancer treatment that thrive in oxygen starved environments have been used successfully to target cancer tumours. Yeast – explosive detector. 27

28. Interesting facts(6) Johns Hopkins researchers have genetically engineered the first mouse that models both the anatomical and behavioral defects of schizophrenia, a complex and debilitating brain disorder that affects over 2 million Americans. 28

29. Conclusions Bioinformatics is the new science, which was created on the intersection of biology and computer science It’s very useful for us, because helps in disease treatment, drugs development and better understanding of our organism It’s divided into different fields, such as genomics, proteomics, etc. For achieving special purpose the different computer methods are used, such as chain-termination method or comparative modeling 29

30. Reference list M.H. Fulekar: Bioinformatics. Applications in life and environmental sciences Venkatarajan Subramanian Mathura,Pandjassarame Kangueane: Bioinformatics: a concept-based introduction http://www.genome.gov/18016863 http://www.wisegeek.com/what-is-genomics.htm http://www.daviddarling.info/encyclopedia/D/DNA_seq uencing.htmlhttp://www.daviddarling.info/encyclopedia/D/DNA_seq uencing.html http://2010.igem.org/files/presentation/Hong_Kong- CUHK.pdfhttp://2010.igem.org/files/presentation/Hong_Kong- CUHK.pdf http://www.eurekalert.org/pubnews.php 30

31. Thank You for attention! Questions ? 31