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

Lectures and exercises Wireless network: https://auth.wireless.dtu.dk/index.cgi Written exam Jan 21 - bring computer, books and notes 4 hour written Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.

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)

Everything is linked from the course programme http://wiki.bio.dtu.dk/teaching/index.php/Course27633autumn2015

Daily teaching overview

Teaching material 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 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) 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

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

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

Genome browsers - Ensembl

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