| Lecturer |
Prof.
Dr. Daniel Huson
|
Time and place
|
Mo
10:20-12:00 h in A301, Sand 13/14 and Wed 11:30-13:15h in Lecture
Theatre 1, Sand 6/7
|
Problem Session 1
|
Wed, 16-18h, small lecture room, Sand 6 |
Problem
Session 2
|
Wed 16-18h, big seminar room, Sand 6
|
Problem
Session 3
|
Thu
8-10h, small seminar room, Sand 6
|
This is part 2 of Algorithms in Bioinformatics. Part 1 can be found here.
Overview and script:
Algorithmic core problems in bioinformatics, including:
0. Introduction
1. Physical Mapping
2. Suffix trees
3. Suffix arrays
4. Protein secondary structure
5. Protein tertiary structure
6. Peptide sequencing *
7. Genome assembly
8. Phylogenetic networks +
9. Specificity
prediction using SVMs *
10. Computational
methods for microRNAs *
11. Motif finding #
11.1
Brute-force motif finding *
12. DNA compression
Download the script here.
*): These topics
will not be part of the oral exam.
+): For the oral exam, you
should understand the concept of compatibility and know what a split
network is. What are consensus networks and how are they computed?
#): What is the planted motif problem? How does Gibbs sampling work?
Assignments:
Assignment #1
Assignment #2
Assignment #3 Java
Assignment #4 Java
Assignment #5 and #6
Java
Assignment #7
Assignment #8 Java
Assignment #9 Java
Assignment #10 Java
Assignment #11
Assignment #12
Assignment #13
|
Teaching