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It og Sundhed Nov. 11 - 27 Jan.

It og Sundhed Nov. 11 - 27 Jan. Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU Mail: tnp@cbs.dtu.dk. Lectures and exercises. Lectures: 9 15 - 12 room 062 Exercises: 13 - 16 room 062 Borrow laptops from CBS for exercises

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It og Sundhed Nov. 11 - 27 Jan.

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

  2. Lectures and exercises Lectures: 915 - 12 room 062 Exercises: 13 - 16 room 062 Borrow laptops from CBS for exercises Wireless network: https://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 Bent Petersen Thomas Nordahl Petersen Kasper Nielsen Rasmus Wernersson Anders Gorm Pedersen 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 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)

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

  12. Phylogenetic tree

  13. Sequence alignment - Blast

  14. 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

  19. Protein 3D-structure

  20. Neural NetworksFrom knowledge to information Biological feature Protein sequence

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

  22. Logo plots

  23. Logo plots

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

  25. Written Exam

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