It og Sundhed Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU

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Presentation transcript:

It og Sundhed Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU

Lectures and exercises Lectures: room 062 Exercises: room 062 Wireless network: Course days once a week (Break during christmas from Dec 15) Written exam Jan Undervisning er på dansk, men undervisningsmateriale er fortrinsvis på engelsk.

Teachers Thomas Nordahl Petersen Henrik Nielsen Anders Gorm Pedersen Bent Petersen Kasper Nielsen Thomas Blicher

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

Everything is linked from the course programme

Readings, slides and hand-outs

Teaching material

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

Outline of the course

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)

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:

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Theory of evolution Charles Darwin

Phylogenetic tree

Sequence alignment - Blast

BLAST Exercise

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

Genome browsers - Ensembl

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

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

Written Exam

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