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Bioinformatik: It og Sundhed - course programme, winter 2010


Teachers:

Curriculum:
The curriculum consists of hand-out notes and the computer exercises themselves. There is no formal text-book. All needed reading material will be available online, linked directly from this page. The material can be read on a day-to-day basis.

Exam:
4 hours written exam.

Where and when:
The Technical University of Denmark, Lyngby Campus, Building 208, room 062 and 060 (From Jan 6'th - 27 Jan). Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions. Map of the DTU buildings here.

The course runs for 10 weeks with lectures and exercises 1 day a week from 9:15 to ~16:00 (or wheneven the computer execersis of the day has been completed).
The exam will be Jan 27'th, 2011 in room 060 - also in the basement close to room 062.
Each day starts with lectures in the morning, and concludes with computer excersices in the afternoon. Teaching will be in danish, but slides and readings are most often in english.


Hardware / Software used

The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. FireFox, Safari or a recent version of Internet Explorer - a browser which supports tabs is recommended) and Java installed. Java is used in some exercises to run visualization software. Link: www.java.com. A computer is necessary for most of the exercises, therefore bring your own. It is possible to borrow a computer at CBS. In that case send a mail ASAP to the course coordinator.

We recomment the JEdit text editor for use on sequence files, since it is well suited for this purpose and is platform independent. Link: www.jedit.org.

For the protein structure exercise the PyMOL software (also cross-platform) will be used. Main link: www.pymol.org.

Free Student's version:

Username/password will be mailed to you by Thomas Blicher

Useful links:

Collection of links: show me

Room: Teaching will be in building 208, room 062 and 060 (downstairs) - unless another place in announced for that teaching-day


Course programme:

Week 45 - Thursday 11th of November

Lecture 1: Introduction to the course - Thomas Nordahl Petersen
Slides: Introduction

Lecture 2: Biological information, DNA structure and sequencing, GenBank searching - Rasmus Wernersson

Readings: GenBank (The yearly GenBank publication, 2008). DNA sequencing tutorial - source: IDT Tech Vault.
Slides: Biological information + DNA data
Hand outs: Chromatogram - GenBank + FASTA format.

Lecture 3: DNA, Amino Acids and Proteins - Thomas Nordahl Petersen
Slides: Powerpoint
Handout: Start codon & DNA/RNA translation table

Exercises
1) Searching the GenBank.
2) Protein Databases.


Week 46 - Thursday 18th of November

Lecture 1: Evolution and DNA

Reading:Brief introduction to evolutionary theory - Anders Gorm Pedersen
Slides: Evolution intro
pdf: Evolution intro

Lecture 2: Amino acids & proteins part II - Thomas Nordahl
Slides: Amino acids & proteins part 2

Exercises
Learning amino acid properties by use of modeling kit - modeling by hand

1) Model building exercise

2) Small quiz - amino acids and their properties (Quiz)


Week 47 - November 25 of November

Lecture 1: Substitution matrices and Log-odds scores - Thomas Nordahl Petersen Slides: ppt
Readings for lecture 1 and 2: p. 35-47

Lecture 2: Global and local alignment - Thomas Nordahl Petersen Slides: ppt

Exercises
1) Sequence alignment the hard way - on paper - Thomas Nordahl Petersen
Exercise: pdf

2) Pairwise alignment


Week 48 - Thursday 2th of December

Lecture 1: Introduction to Blast - Thomas Nordahl Petersen
Slides: BLAST powerpoints
Handouts: BLOSUM62 matrix - BLASTN heuristics - BLASTP heuristics.

Lecture 2: Psi-Blast - Iterative Blast searches and Position Specific Scoring Matrices - Bent Petersen
Slides: PowerPoint slides.

Readings: Page 68-80 in Immunological Bioinformatics (PDF - extract from the Book - password protected)

Exercises
1) Using BLAST for sequence searches - Thomas Nordahl Petersen


Week 49 - Thursday 9th of December

Lecture 1: Mutiple alignments - Anders Gorm Pedersen
Slides: PowerPoint slides (PDF).
Readings: Mutiple Sequence Alignment (Short software review paper)
Readings:RevTrans (Short paper on an apporach which mixes DNA and protein alignment)

Exercise 1: Multiple Alignments - Anders Gorm Pedersen / Rasmus Wernersson

Lecture 2: Phylogenetic trees - Anders Gorm Pedersen
Slides: PowerPoint slides (PDF).
Readings: Introduction to Treebuilding (PDF) - Evolutionary trees (except the section "How to reconstruct an evolutionary tree").
Hand-outs: handout exercise Reconstruction of a distance tree

Exercise 2: Phylogenetic Trees - Anders Gorm Pedersen / Rasmus Wernersson


Week 50 - Thursday 16th of December

Lecture 1: Genome Browsers - Thomas Nordahl Petersen
Readings:UCSC Genome Browser, Update 2008
Slides: PowerPoint slides

Lecture 2: From genotype to phenotype - Kasper Nielsen
Slides: pdf


Exercises
1) Using the UCSC genome browser - Thomas Nordahl Petersen
2) Genotype2PhenotypeLite - Kasper Nielsen


Week 1 - Thursday 6th of January (room 060)

Lecture 1: Protein 3D-structure - Thomas Blicher
Readings: Protein Structure (Wikipedia - Frozen version).
Link to "Live" version: http://en.wikipedia.org/wiki/Protein_structure
Slides: Protein structure

Lecture 2: Homology modelling - Thomas Blicher
Slides; Homology modelling

Exercises
1) PDB and PyMOL - Thomas Blicher


Week 2 - Thursday 13th of January (room 060)

Lecture 1: Introduction to neural networks - Thomas Nordahl Petersen
Slides: PowerPoint

Lecture 2: Sequence based predictors. Secondary structure and surface accessibility - Bent Petersen
Slides: PowerPoint
pdf
Keynote


Exercises
1) SignalP, NetSurfP and Propepdide predictions - Thomas Nordahl
exercise


Week 3 - Thursday 20th of January (room 060)

Lecture 1: Entropy, Information Content & logo plots - Thomas Nordahl Petersen
Readings Page 69-80 in chapter 4:pdf
Readings:WebLogo
Slides: PowerPoint
Handout:Example how to calculate frequencies and make Logo

Lecture 2: Summary - Thomas Nordahl Petersen
Slides: PowerPoint

Exercises
1) Logo plots - Thomas Nordahl Petersen
exercise


Week 4 - Thursday 27th of January (room 060)

Written Exam from 9-13 - kom i tide 8:45. Medbring egen laptop, kuglepen/blyant evt viskelaedder. Besvarelser til eksamen skal du aflevere skriftligt.
Du mà benytte internet under eksamen.



Eksamen_27-1-2011




Questions from last years oral exam

Questions from last years oral exam



Spørgsmål 1

Spørgsmål 2

Spørgsmål 3

Spørgsmål 4

Spørgsmål 5