Thomas Nordahl Petersen, Associate Prof, Food DTU Sundhed og Informatik Thomas Nordahl Petersen, Associate Prof, Food DTU Building 204, room 105 Mail: tnpe@food.dtu.dk
Lectures and exercises Lectures+Exercises: 9:15 – 12:00 Wireless network: https://auth.wireless.dtu.dk/index.cgi Written exam Dec 20, 2018 - bring computer, books and notes 4 hour written Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk. Course program: http://teaching.bioinformatics.dtu.dk/36633/index.php
Teachers Thomas Nordahl Petersen Henrik Nielsen Anders Gorm Pedersen
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)
Teaching material 5
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
Outline of the course
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
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
Theory of evolution Charles Darwin 1809-1882 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Charles Darwin 1809-1882
Phylogenetic tree
Sequence alignment - Blast
Sequence alignment - Blast
BLAST Exercise
Protein 3D-structure
Protein 3D-structure
Neural Networks From knowledge to information Protein sequence Biological feature
Prediction of biological features Surface accessible Predict surface accessible from amino acid sequence only.
Logo plots
Logo plots
Logo plots Information content, how is it calculated - what does it mean.
Written Exam