Algorithms in Bioinformatics


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Algorithms in Bioinformatics 2

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

 

 

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