1. Thomas Nordahl Petersen, Associate Bioinformatics, DTU
Sundhed og Informatik
Thomas Nordahl Petersen, Associate Bioinformatics, DTU
Building 208, room 021
Mail:

2. Lectures and exercises
Lectures+Exercises: 9:15 – 12:00
Wireless network:
Written exam Dec 21, bring computer, books and notes
4 hour written
Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.
Course program:

3. Teachers
Thomas Nordahl Petersen
Henrik Nielsen
Anders Gorm Pedersen

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. Teaching material 5

6. 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
Genotype, phenotype & SNP’s
Protein 3D-structure
Artificial neural networks
Practical use of bioinformatics tools
Sequence information and Logo plots

7. Outline of the course

8. The Amino Acids Thr (T) Phe (F) Val (V) Ala (A) His (H) Arg (R)
Ser (S)
Leu (L)
Cys (C)
Met (M)
Asp (D)
Lys (K)
Asn (N)
Ile (I)
Trp (W)
Gln (Q)
Glu (E)
Tyr (Y)
Pro (P)
Gly (G) 8

9. 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:

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

11. Phylogenetic tree

12. Sequence alignment - Blast

13. Sequence alignment - Blast

14. BLAST Exercise

15. Protein 3D-structure

16. Protein 3D-structure

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

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

19. Logo plots

20. Logo plots

21. Logo plots
Information content, how is it calculated - what does it mean.

22. Written Exam