Algorithms in Bioinformatics - Q1

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Announcements

• 21/10/08: Exam schedule available (see below under Exam).
• 02/10/08: Exam questions available.
• 02/10/08: Schedule for week 7 is avalable.
• 26/09/08: Schedule for week 6 is available.
• 22/09/08: Description of Mandatory Project 2 available.
• 22/09/08: The exam will be on October 27 in Shannon-164.
• 22/09/08: Schedule for week 5 is available (sorry for the delay).
• 04/09/08: Schedules for week 3 and 4 are available.
• 03/09/08: Description of Mandatory Project 1 available.
• 29/08/08: Schedule for week 2 is available.
• 07/08/08: Schedule for week 1 is available.
• 06/08/08: Initial www-page 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 for analysis of biological sequences. The class introduces the underlying biological questions and models, but concentrate on algorithmic problems and computational techniques in relation to comparison of two or more biological sequences; searching in sequence databases; gene structure prediction; and analysis of whole genomes.

See official course description.

Schedule

Lectures take place:

• Wednesday 13.15-16.00, Shannon-164.

First lecture is on Wednesday, August 27 in Shannon-164.

The tentative plan is:

• Week 1: Biological sequences and global pairwise alignment (with linear and affine gapcost)
• Week 2: Local pairwise alignment. Techniques for saving space
• Week 3: Comparison of whole genomes
• Week 4: Multiple sequence alignment, exact methods
• Week 5: Speeding up the computation of an alignment
• Week 6: HMMs in bioinformatics
• Week 7: Multiple sequence alignment, heuristics

Literature

We will use research papers and excerpts from text books which will be 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.

List of exam question and curriculum.

The exam takes place on Monday, October 27, in Shannon-164, from 09:00, according to this exam schedule.

Lecturer

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

Christian Nørgaard Storm Pedersen

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