1. 1 Rong-I Hong, D.Phil. An Overview for Bioinformatics Rong-I Hong, D.Phil. Biomedical Engineering Center Industrial Technology Research Institute RI_Hong@itri.org.tw

2. 2 Rong-I Hong, D.Phil. rWhat is bioinformatics in your mind now? rWhy do you want to take this bioinformatics course? rWhat do you expect from this course?

3. 3 Rong-I Hong, D.Phil.

4. 4 How Genes Work? Source: The Economist 356, 56 (2000)

5. 5 Rong-I Hong, D.Phil. Central Dogma rData Storage and Information Flow n DNA n RNA n Protein replication transcription translation

6. 6 Rong-I Hong, D.Phil. Biological Macromolecules n DNA n RNA n Protein

7. 7 Rong-I Hong, D.Phil. Bioinformatics rBioinformatics  Solving the biological problems with IT. r IT  Hardware  Software r E-business  Hardware  Software  Content  Application

8. 8 Rong-I Hong, D.Phil. Data Storage & Information Flow n DNA n RNA n Protein replication transcription translation Biological Function Pharmaceutical Implication Healthcare Significance

9. 9 Rong-I Hong, D.Phil. Logical Flow rDatabase rAlgorithms rApplications SequenceStructureFunction

10. 10 Rong-I Hong, D.Phil. integration Doing Biology with Engineering - IT & Chip Technology n Excessive Biochemical Data

11. 11 Rong-I Hong, D.Phil. Database rPrimary Protein Database (Sequence or Structure)  Swiss Prot (sequence) and PDB (structure). rProcessed Protein Database (Sequence or Structure)  Pfam (sequence) and SCOP (structure). rGene Database (Sequence)  GenBank (sequence) and UniGene (transcript map).  Genomes  EST rMetabolism and Pathways  BRITE, PathDB rValue-added Database rText and Knowledge

12. 12 Rong-I Hong, D.Phil. Algorithms rLanguage Theory rStatistical Analysis rHidden Markov Model rNeural Network rArtificial Intelligence and Machine Learning rGenetic Algorithms rDynamics Programming

13. 13 Rong-I Hong, D.Phil. Applications rSequence Analysis  Database Searching and Multiple Sequence Alignments  Phylogene Analysis  Gene Finding and Prediction  Gene Annotation and Assembly rStructure/Function Analysis  Structural Comparison  Structure/Function Prediction  Protein Design

14. 14 Rong-I Hong, D.Phil. Applications rExperiment Data Analysis  Gene Expression Profiling  Proteomics Analysis  Intermolecular Interactions rKnowledge Management  Text Comparison  Natural Language Processing  Data Mining

15. 15 Rong-I Hong, D.Phil. Bioinformatics Spectrum

16. 16 Rong-I Hong, D.Phil. 512 CPUs, 128 Nodes 507.6 GFLOPS #31 on the Top500 List AlphaServer SC/Tru64 UNIX at LLNL Hardware

17. 17 Rong-I Hong, D.Phil. QUIZ rBriefly picture what the bioinformatics looks like in your mind before and after this lecture. rFind you partner in the opposite background, i.e. (math to bio) or (bio to math), work as a team throughout this semester.

18. 18 Rong-I Hong, D.Phil. References rIntroduction to Bioinformatics  T. K. Attwood and D. J. Parry-Smith  ISBN: 0-582-32788-1  Longman  Chapters 1, 2, 3 and 4.