Biological Sequence Analysis (6 cr, 3 cu)
News
- Course results
- Exam points
- Course Exam on Wednesday February 28 at 16-19 in A111 will cover Chapters 1 - 7 from Durbin et al book. However, subsections 4.5, 5.6, 5.8 and 7.6 are NOT included in the exam.
- Exercise session 3 (6.2.) starts immediately after the lecture at 16:05!
- Exercise solutions added to the course folder
- Chapter 11 and errata of the book [1] added to the course folder
- Lecture notes and first 8 chapters of the book [1] are available for copying in room C127
- Lectures start on January 15th!
Course Prerequisites
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Data structures, Basic skills in probability or statistics
Lectures
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Prof. Esko Ukkonen | 15.01.-20.02. | Monday 14-16, Tuesday 14-16 | D122
Exercise sessions
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MSc. Pasi Rastas | 22.01.- 23.02. | Tuesday 16-18 | CK107
- If you cannot participate Tuesdays exercise session, you may return your exercise solutions electronically or on paper to Pasi Rastas (by Tuesday at 16.15)
- 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:
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[1] Text book: R. Durbin, S. Eddy, A. Krogh & G. Mitchinson: Biological Sequence Analysis. Cambridge University Press 1998 (errata).
- 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
- Chapter 7: Building phylogenetic trees
- Chapter 8: Probabilistic approaches to phylogeny
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Course will cover (in some detail) chapters 1-8 from textbook [1]:
Grading
- 60 points maximum
- exercise activity 10 points
- exam 50 points
Exam
- Wednesday 28th of February from 16.00 to 19.00 in A111, Exactum
Pasi Rastas Last modified: Tue Mar 20 12:17:50 EET 2007