Algorithms for Bioinformatics

582670
4
Bioinformatics
Intermediate studies
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. Prerequisites: programming skills. Course book: Neil C. Jones and Pavel A. Pevzner: An Introduction to Bioinformatics Algorithms, MIT Press, 2000.

Exam

21.10.2014 09.00 A111
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

Group: 1
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

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:

Week 2:

Week 3:

Week 4:

Week 5:

Week 6:

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.