1. It og Sundhed Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU Building 208, room 021 Mail:tnp@cbs.dtu.dktnp@cbs.dtu.dk

2. Lectures and exercises Lectures: 9 15 – 12 Exercises: 13 – 16 Wireless network: https://auth.wireless.dtu.dk/index.cgihttps://auth.wireless.dtu.dk/index.cgi Written exam Jan 21 - bring computer, books and notes 4 hour written exam from 9-13 room S01 (i stuen), building 101A Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.

3. Teachers Thomas Nordahl Petersen Henrik Nielsen Anders Gorm Pedersen Bent Petersen Thomas Blicher

4. This is a hands-on course Lectures are giving the background/theory of a bioinformatics topic –The exercises are giving you a hands-on experience the that topic Example Theory of sequence alignment –Alignment by hand, filling out scoring matrices Learning about the amino acids –Building amino acids by hand (Model building)

5. Everything is linked from the course programme http://wiki.bio.dtu.dk/teaching/index.php/Course27633autumn2012

6. Readings, slides and hand-outs

7. Teaching material

8. 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 Genotype, phenotype & SNP’s –Protein 3D-structure & homology modeling –Artificial neural networks & case stories –Practical use of bioinformatics tools –Sequence information and Logo plots

9. Outline of the course

10. 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)

11. 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

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

13. Phylogenetic tree

14. Sequence alignment - Blast

16. BLAST Exercise

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

18. Genome browsers - Ensembl

19. Protein 3D-structure

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

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

23. Logo plots

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

26. Written Exam