Introduction to bioinformatics - Turbo version - Course program 2012

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Introduction to bioinformatics - Turbo version >> Course program 2012

General information


The Technical University of Denmark, Lyngby Campus, Building 208, Room 062. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.


The course runs from Friday the 1st of June to Friday the 22nd of June, from 9:15 to ~16:30 (or whenever the computer exercises of the day have been completed). There will be no class on June 5 (Constitution Day). During the first week, we will start each day with lectures in the morning, and conclude with computer exercises in the afternoon. The second and third weeks will be dedicated to group project work.

Course materials:

The course materials include hand-out notes and the computer exercises themselves. There is no formal textbook. All needed reading material will be available online, linked directly from this page. The material can be read on a day-to-day basis.


Project work will culminate in a poster presentation on Friday, 22 June. Grades will be based on exercises and on the project (poster presentation).

Required hardware / software

The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. Firefox, Safari or Internet Explorer) and Java installed. Java is used in some exercises to run visualization software. Link:

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

For the protein structure exercise the PyMOL software (also cross-platform) will be used. Link:

Free Student's version: On Campusnet

If necessary, a username/password will be mailed to you, or provided at the course.


Working in groups is allowed. Each group has to keep a text document with answers to the questions asked in the exercises. After completing an exercise, upload it via Campusnet under the given day. Remember to state the members of the group so everyone can get credited; one submission per group is enough. All exercises have to be handed in on the day when it was assigned. Late exercises will receive half credit.

The submitted document should be kept as minimalistic as possible - the important thing here is to focus on giving a nice and simple overview of your answers and not to spend a lot of time on fancy formatting. For example:

Answers to the Multiple Alignment exercise
Report by: Rasmus Wernersson (v18103) 

Question 1
Fasta format file: 


Question 2
2a): xxxx yyyy zzzz
2b): ddd jjj uuu

Lecture Plan 2012

Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!

Friday 1 June

9.15 - 9.30 - Introduction to the course - Aron Charles Eklund & Bent Petersen

Lecture 1 - Evolution and DNA - Anders Gorm Pedersen

Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
Slides (PDF):

Lecture 3 - Proteins - data and databases - Henrik Nielsen.
Slides (PDF):

Exercises - (Exercise helper: Asli Ozen)
  1. Exercise: Searching the GenBank database
    Note: you don't have to answer question 1.3 about line endings and question 3 (the "Free exercise")! - (Answers)
  2. Exercise: Translation - Virtual Ribosome - (Answers)
  3. Exercise: The protein database UniProt - (Answers)

Monday 4 June

Lecture 1 - Pairwise alignment - Rasmus Wernersson
  • Page 35-55 in Immunological Bioinformatics (PDF - extract from the Book - on Campusnet in the folder "Reading materials")
Handout exercise:
Lecture 2 - Introduction to BLAST - Rasmus Wernersson
Exercises: (Exercise helper Rachita Yadav)
  1. Pairwise alignment - (Answers)
  2. BLAST - (Answers)

Tuesday 5 June

Constitution Day -- no class.

Wednesday 6 June

NOTE! Class will be in Building 306 room 96

Lecture 1 - Multiple alignment - Anders Gorm Pedersen
Slides: PDF
Exercise: Multiple alignment (Exercise helper: Francesco Favero) - (Answers )

Lecture 2 - Phylogenetic trees - Anders Gorm Pedersen
Slides: PDF
Exercise: Phylogenetic trees (Exercise helper: Francesco Favero) - (Answers)

Lecture 3 - Protein 3D structure - Thomas Blicher
Exercises: (Exercise helper: Francesco Favero)
  • PDB and PyMOL - Only exercise 1. - (PDF Answers)
  • IMPORTANT: Remember to bring a three-button mouse for the exercise. The middle button on the mouse should be a clickable scroll-wheel (most scroll-wheels are).

Thursday 7 June

Lecture 1 - PSI-BLAST - Morten Nielsen
Lecture 2 - Prediction methods in immunological bioinformatics - Morten Nielsen
Exercises: (Exercise helper Salvatore Cosentino)
  1. PSI-BLAST - (Answers)
  2. HCV vaccine development - (Answers)

Friday 8 June

9.15 - 9.45: Special lecture - MetaGenomic Species - learning structure from metagenomics - H. Bjørn Nielsen

9.45 -10.15: Introduction to projects - Aron Charles Eklund and project leaders.

Lecture 1 - Functional Human Variation Agata Wesolowska
Exercise 1: (Exercise helper Agata Wesolowska)

Lecture 2 - Human Genome Browser - Thomas Nordahl Petersen

Exercise 2 (Exercise helper Josef Korbinian Vogt)
Exercise 2 (answers)

Monday 11 June – Thursday 21 June

Work in groups on projects.
Posters (as a PDF file) must be submitted to CampusNet by 12:00 noon on Thursday, 21 June.

Friday 22 June

09:15 - Poster session and oral examination inside the main entrance to building 208 (upstairs from the classroom).


Groups of 3-5 individuals will form a project team. The following three projects are available, with separate project leaders. Project preferences will be collected, and projects will be allocated, with an attempt to match preferences.

NOTE: Projects are subject to change.


Project 1 - Non-synonymous mutations and cancer (Aron Eklund)

Cancer is a genetic disease in which the tumor cell's genome is altered relative to the patient's normal genome. Several genes are frequently found mutated in cancer, suggesting that the mutation may change the gene's function to give the tumor cell a selective advantage. This project involves analysis of tumor-associated gene mutations in order to understand how the mutation causes or enables cancer development.

Project 2 - Polymorphism of human cytochrome P450 enzymes and their roles in drugs efficacy and adverse effects (Olivier Taboureau)

A study of how interindividual variations in the DNA sequence of cytochrome P450 enzymes (CYPs) affect drug response. The human CYP super family contains 57 functional genes and 58 pseudogenes playing an important role in the metabolism of therapeutic drugs, xenobiotics and endogenous compounds. Based on the sequences of the 57 functional genes, the team should develop a multiple sequence alignment and a phylogenetic tree. By integrating information from several bioinformatics and chemoinformatics web resources, the effect of Single Nucleotides Polymorphisms (SNP) on efficacy and adverse effects of drugs will be studied.

Project 3 - Immunological bioinformatics (Morten Nielsen)

The immune system normally does a good job of keeping us free from diseases, but sometimes it fails. One approach towards understanding why this happens is to produce advanced simulation models of the immune system and to understand the relationship between hosts and patogens in this manner. Depending on the complexity of these models and the input given, they can be used to simulate what happens when a host gets infected by a pathogen, thereby predicting the co-evolvement of pathogens and immune systems. One aim of the modeling is to identify parts of proteins known as epitopes which are recognized by the immune system, thereby inducing a protective response. This knowledge is very valuable in the development of better vaccines and provides very important insights into the nature of cancer, allergy and autoimmune diseases.