Biological Sequence Analysis (6 cr, 3 cu)
News
- Lectures start on October 27th!
- Course registration via Ilmo (if you have problems in registration, please contact Pasi Rastas)
- Lecture on Monday 10.11. moved to Wednesday 12.11. at 16-18 in C222.
- Example solutions for exercise sets 1 and 2 are now in the course folder.
- Lecture room on Mondays has changed to C222!
- Example solutions for exercise sets 3 and 4 are now in the course folder.
- Extra exercise session on Monday 8.12. at 14-16 in C221 (does not affect exercise points).
Course Prerequisites
-
Data structures, Basic skills in probability or statistics
Lectures
-
Prof. Esko Ukkonen | 27.10.-04.11. | Monday 14-16, Tuesday 14-16 | C221
Prof. Esko Ukkonen | 11.11. | Tuesday 14-16 | C221
Prof. Esko Ukkonen | 12.11. | Wednesday 16-18 | C222
Prof. Esko Ukkonen | 17.11.-01.12. | Monday 14-16 | C222
Prof. Esko Ukkonen | 18.11.-02.12. | Tuesday 14-16 | C221
Exercise sessions
-
MSc. Pasi Rastas | 6.11.-04.12. | Thursday 12-14 | C220
-
MSc. Pasi Rastas | 08.12. | Monday 14-16 | C221 (extra exercise session)
- If you cannot participate exercise session, you may return your exercise solutions electronically or on paper to Pasi Rastas (by Thursday at 12.15)
- To be eligible to take the exam you have to solve at least 50 percent of the total number of exercise problems. If you solve more than that you'll get 0..10 points such that solving 80 percent or more gives full 10 points
Course material:
All course material, including the lecture notes, is available in the course folder in room C127-
Text book: R. Durbin, S. Eddy, A. Krogh & G. Mitchinson:
Biological Sequence Analysis. Cambridge University Press 1998
(errata (MS Word)).
-
Course will cover (in some detail) chapters 1-6 from textbook [1]:
- Chapter 1: Introduction
- Chapter 2: Pairwise alignment
- Chapter 3: Markov chains and hidden Markov models
- Chapter 4: Pairwise alignment using HMMs
- Chapter 5: Profile HMMs for sequence families
- Chapter 6: Multiple sequence alignment methods
- Text book: Paul H. Dear (ed.): Bioinformatics (Methods Express) Scion Publishing Ltd Sep. 2007.
- Chapter 6: Finding regulatory elements in DNA sequence. Available online here.
- Molecular Biology Primer (slides from N. Jones and P. Pevzner: An Introduction to Bioinformatics Algorithms)
- S Henikoff and J G Henikoff: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992 November 15; 89(22): 10915 -10919.
Grading
- 60 points maximum
- exercise activity 10 points
- exam 50 points
Exam
- Thursday 11th of December from 16.00 to 19.00 in A111, Exactum.
Pasi Rastas Last modified: Thu Dec 4 15:19:49 EET 2008