Department information

 

Biological Sequence Analysis (6 cr, 3 cu)

News

• New material on BLOSUM matrices: Original PNAS article by Henikoff & Henikoff and more elaborate description in Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology by Dan Gusfield. Relevant parts are available in the course folder.
• The course will have just one exercise session on Monday.

Course Prerequisites

Data structures, Basic skills in probability or statistics

Lectures

Prof. Esko Ukkonen | 14.01.-19.02. | Monday, Tuesday 14-16| D122

Exercise sessions

PhD. Kimmo Palin | 21.01.- 22.02. | Monday 12-14 | C221

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In case of emergency, you can participate in the exercises by sending your answers by e-mail to Kimmo Palin before the actual exercise session. The deadline is Monday noon!
• 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

1. 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
2. Text book: Paul H. Dear (ed.): Bioinformatics (Methods Express) Scion Publishing Ltd Sep. 2007
   • Chapter 6: Finding regulatory elements in DNA sequence
3. Molecular Biology Primer (slides from N. Jones and P. Pevzner: An Introduction to Bioinformatics Algorithms)
4. 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

• Friday 29.2. 16:00-18:30 in A111

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Kimmo Palin

Last modified: Mon Feb 18 16:08:49 EET 2008