Algorithms in Bioinformatics - Q1

• Main Page
• Weekly Schedule
• Mandatory Projects
• List of Participants

Announcements

• 10/10/07: If you do the multiple alignment project, you are welcome to use spdist3.py for debugging your own implementation of computing the score of an optimal SP multiple alignment. The program spdist3.py is a very naive and straightforward implementation of computing the optimal SP score of an multiple alignment of three sequences. I do not guarantee its correctness. You are also welcome to look at spdist.py which can align any number of sequences and also print an optimal alignment. Again, I do not guarantee its correctness.
• 04/10/07: Schedule for week 7 is available.
• 28/09/07: Schedule for week 6 is available.
• 25/09/07: The exam will be held on Monday, October 29. See below under "Exam" for more info.
• 25/09/07: A (preliminary) description of mandatory project 2 is available.
• 25/09/07: Look at affine_problem.txt for an illustration of the problem that occurs when implementing affivne gap cost in linear space.
• 20/09/07: Schedule for week 5 is available.
• 03/09/07: Schedule for week 3 and week 4 is available.
• 03/09/07: A (preliminary) description of mandatory project 1 is available.
• 29/08/07: Schedule for August 31 and week 2 is available.
• 29/08/07: Time and place for lectures have changed to Tuesdays 8-9 and Fridays 13-15 in Shannon-157. First lecture according to the new schedule will be on Friday, August 31.
• 21/08/07: Schedule for week 1 is available.
• 07/08/07: Time and places for lectures available.
• 02/07/07: 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:

• Tuesdays 08.15-09.00, Shannon-157.
• Fridays 13.15-15.00, Shannon-157.

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: Speeding up the computation of a global alignment.
• Week 4: Multiple sequence alignment
• Week 5: Hidden Markov models
• Week 6: Computational gene finding
• Week 7: Comparison of whole genomes

Check the weekly schedule for information about each lecture.

Literature

We will use research papers and excerpts from text books which will be made available for download.

Exam and Projects

Each student must participate in a series of mandatory projects in order to qualify for the exam. The projects can be done in groups of 2-3 students.

The final exam is an individual oral exam (20 minutes without preparation time) where you give a presentation of a exam question related to one of the mandatory projects. The question is chosen randomly among four exam questions. For each question you should prepare a 10-12 minutes presentation covering (at least) the topics mention in the question.

List of exam question and curriculum.

The exam takes place on Monday, October 29, in Shannon-157, from 09:00, 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: 090.112
Phone: +45 8942 3121
E-mail: cstorm [at] daimi.au.dk