1. It og Sundhed Nov. 11 - 27 Jan. Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU Mail:tnp@cbs.dtu.dktnp@cbs.dtu.dk

2. Lectures and exercises Lectures: 9 15 - 12 room 062 Exercises: 13 - 16 room 062 Borrow laptops from CBS for exercises Wireless network: https://auth.wireless.dtu.dk/index.cgihttps://auth.wireless.dtu.dk/index.cgi Course days once a week (not weeks 51 & 52) Written exam Jan 27 - 2011 (room 062), bring a computer. Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.

3. Teachers Thomas Nordahl Petersen Rasmus Wernersson Anders Gorm Pedersen Bent Petersen Kasper Nielsen Thomas Blicher

4. This is a hands-on course The major part of the course is computer exercises We get to use the actual methods We get to use “live” online database

5. Everything is linked from the course programme

6. Readings, slides and hand-outs Power point presentations are uploaded when ready. Updated versions are available the day after.

7. Outline of the course Topics will cover a general introduction to bioinformatics –Evolution –DNA / Protein and amino acids –Alignment and scoring matrices How does it work & what are the numbers –Visualization of multiple alignments Phylogenetic trees and logo plots –Commonly used databases Uniprot/Genbank & Genome browsers –Protein 3D-structure & homology modeling –Artificial neural networks & case stories –Practical use of bioinformatics tools –Sequence information and Logo plots

8. Outline of the course

9. The Amino Acids Asn (N) Asp (D) Gln (Q) Glu (E) His (H) Lys (K) Arg (R) Tyr (Y) Trp (W) Phe (F) Gly (G) Pro (P) Ile (I) Met (M) Leu (L) Ala (A) Val (V) Ser (S) Cys (C) Thr (T)

10. Automated sequencing The major break-through of sequencing has happended through automation. Fluorescent dyes. Laser based scanning. Capillary electrophoresis Computer based base- calling and assembly. Images: http://www.idtdna.com/support/technical/TechnicalBulletinPDF/DNA_Sequencing.pdf

11. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Theory of evolution Charles Darwin 1809-1882

12. Phylogenetic tree

13. Sequence alignment - Blast

15. BLAST Exercise

16. Genome browsers - UCSC Intron - Exon structure Single Nucleotide polymorphism - SNP

17. Genome browsers - Ensembl

18. Protein 3D-structure

20. Neural Networks From knowledge to information Protein sequence Biological feature

21. Prediction of biological features Surface accessible Predict surface accessible from amino acid sequence only.

22. Logo plots

24. Information content, how is it calculated - what does it mean.

25. Written Exam