Algorithms for Bioinformatics
Exam
Year | Semester | Date | Period | Language | In charge |
---|---|---|---|---|---|
2014 | autumn | 02.09-16.10. | 1-1 | English | Juha Kärkkäinen |
Lectures
Time | Room | Lecturer | Date |
---|---|---|---|
Tue 12-14 | C222 | Juha Kärkkäinen | 02.09.2014-16.10.2014 |
Thu 12-14 | C222 | Juha Kärkkäinen | 02.09.2014-16.10.2014 |
Exercise groups
Time | Room | Instructor | Date | Observe |
---|---|---|---|---|
Tue 10-12 | B222 | Juha Kärkkäinen | 08.09.2014—17.10.2014 |
General
The course introduces some basic algorithmic concepts and techniques through motivation by selected computational molecular biology problems. The goal is to obtain a solid basis for advanced studies in bioinformatics.
Topics covered: Exhaustive search and motif finding, Greedy algorithms and genomic rearrangements, Dynamic programming and sequence alignment, Graph algorithms and DNA sequencing, Distance-based clustering and phylogeny
Prerequisites: programming skills.
Completing the course
The course consists of lectures, study groups, and exercises, as follows:
First week
- Tue 12-14 - First lecture (introductory)
- Thu 12-14 - Second lecture
Other weeks
- Tue 10-12 - Exercise session on the previous week's topics
- Tue 12-14 - Study group meeting, aiming at an in-depth coverage of the previous week's topics. This is mandatory; in case you cannot attend for contact me personally.
- Thu 12-14 - Lecture
Lectures end with a list of topics and their assignments to the students. The assigned topic is to be studied carefully before gathering to the study group meeting on Tuesday, with the fellow students studying the same topic, to form a common understanding of the assigned topic. Then the groups will be mixed so that each group has an expert from each topic, and the rest of the Tuesday's study group is devoted to teaching each others the material adopted. The exercise session tests the understanding of all topics.
There will be an exam giving 48 points at the maximum. Active participation to exercises gives at the maximum 12 points (30%->1p,85%->12p, linear scale). You need at least 1p from the exercise seesion to enter the exam. The grading is then based on the total points (maximum 60) achieved (~30 points -> 1 and ~50 points -> 5, depending on the difficulty of the exam).
Course Exam
- Tue 21.10.2014 at 9:00 in Exactum hall A111.
- Please check that the number of exercises registered for you are correct.
- Your feedback on improving the course is greatly appreciated. Please use this anonymous feedback form.
- Grounds for grading. Contact the lecturer to see your exam paper and to get feedback.
Renewal/separate exam
- Tue 02.12.2014 at 16:00 in Exactum hall B123.
- This is graded both as a renewal exam (max. 48 points for exam plus max. 12 points for exercises as in the course exam) and as a separate exam (max. 60 points for exam) and the better of the two grades is chosen. The maximum score in the exam is 60 points and the corresponding renewal exam score is obtained by multiplying the score by 0.8.
- There are other separate exams later but this is the only renewal exam.
Literature and material
Lecture notes, exercise problems and other material will added here during the course.
Week 1:
- Molecullar Biology Primer (Tue 02.09.)
- Introductory Lecture (Tue 02.09. 12-14)
- Some videos: The Inner Life of a Cell, Illumina Sequencing Technology
- Lecture 2: Exhaustive search and motif finding (Thu 04.09. 12-14)
Week 2:
- Exercise session 1 (Tue 09.09. 10-12): Problems
- Study group meeting 1 (Tue 09.09. 12:30-14). Assignments are given on slides 28-29 of Introductory Lecture and on slides 79-81 of Lecture 2: Exhaustive search and motif finding.
- Lecture 3: Greedy algorithms and genomic rearrangements (Thu 11.09. 12-14)
Week 3:
- Exercise session 2 (Tue 16.09. 10-12): Problems
- Study group meeting 2 (Tue 16.09. 12:30-14). Assignments are given on slides 49-51 of Lecture 3.
- Lecture 4: Dynamic Programming and Sequence Alignment (Thu 18.09. 12-14 C222)
Week 4:
- Exercise session 3 (Tue 23.09. 10-12 B222): Problems
- Study group meeting 3 (Tue 23.09. 12:30-14 C222). Assignments are given on slides 33-35 of Lecture 4.
- Lecture 5: Graph Algorithms and DNA Sequencing (Thu 25.09. 12-14 C222)
Week 5:
- Exercise session 4 (Tue 30.09. 10-12 B222): Problems
- Study group meeting 4 (Tue 30.09. 12:30-14 C222). Assignments are given on slides 30-32 of Lecture 5.
- Lecture 6: Distance based clustering and phylogeny (Thu 10.02. 12-14 C222)
Week 6:
- Exercise session 5 (Tue 07.10. 10-12 B222): Problems
- Study group meeting 5 (Tue 07.10. 12:30-14 C222). Assignments are given on slides 35-37 of Lecture 6.
- Guest lecture (Thu 09.10. 12:15-13:00 C222): Leena Salmela: Assembling a butterfly genome
- Final notes on the course (Thu 09.10. 13:15-14 C222)
Week 7:
- No program
Week 8:
- Exam (Tue 21.10. 09-12 A111)
Course book
Neil C. Jones & Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms (MIT Press, 2004). It is not necessary to purchase the book, but the course will follow a similar structure.
The book seems to be freely available here: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.218.3258 (click on the PDF icon on the right) or directly here. A local copy is here.