Algorithms in Bioinformatics - Q2

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• Projects

Announcements

• 04/12/08: Schedules for week 6 and 7 are available.
• 28/11/08: Description of mandatory project 2 is available.
• 28/11/08: Schedule for week 5 is available.
• 20/11/08: Schedule for week 4 is available.
• 14/11/08: Schedule for week 3 is available.
• 05/11/08: Schedule for week 2 is available.
• 03/11/08: Description of mandatory project 1 is available.
• 28/10/08: Initial www-pages ready.

About

Bioinformatics is an interdisciplinary area focusing on developing and utilizing algorithms and computer programs for analyzing biological data. Due to extremely efficient biotechnological methods for gathering biological data, the amount of available data grows much faster than the growth in available computational power. Making sense of the collected data thus requires efficient algorithmic and computational techniques.

This class covers central algorithmic problems and computational techniques in phylogenetics and molecular structure prediction. The class introduces the underlying biological questions and models, but concentrates on algorithmic problems and computational techniques in relation to reconstruction and comparison of phylogenetic trees; RNA secondary structure prediction with and without pseudoknots; protein secondary and tertiary structure prediction.

See official course description.

Schedule

Lectures take place:

• Tuesday 12.15-15.00, IT-Huset-112.

First lecture is on Tuesday, November 4 in IT-Huset-112.

Check the weekly schedule for information about each lecture.

The tentative plan is:

• Week 1: Protein folding (in the HP model)
• Week 2: Prediction of RNA 2nd structure
• Week 3: Prediciton of transmembrane helices
• Week 4: Evolutionary trees
• Week 5: Distance based tree reconstruction methods
• Week 6: Character based tree reconstruction methods
• Week 7: Misc

Literature

We will use research papers and excerpts from text books which will be handed out in class or made available for download.

Exam and Projects

To participate in the final oral exam each student must complete all mandatory projects.

The final exam is an individual oral exam (20 min) which includes a discussion related to one of the mandatory projects followed by a general discussion of related topics. The question is chosen randomly among four exam questions. For each question you should prepare a 12-15 minutes presentation.

List of exam question and curriculum.

The exam takes place on Tuesday, January 20, in Shannon-164, from 10:00 according to this exam schedule.

Lecturer

If you have any comments or questions related to the course, do not hesitate to contact me:

Christian Nørgaard Storm Pedersen

Office: 1110.325
Phone: +45 8942 3121
E-mail: cstorm [at] birc.au.dk