Lecturer	Prof. Dr. Daniel Huson
Office hours	Mondays 16-18h, office C310a, Sand 14
Time	Lectures Mo 10-12 h, Wednesday 11-13 h Tutorials: Thursdays, 15-17h (in "Large Lecture Theater" Sand 6/7) Tuesdays, 12-14h (in A104) Thursdays, 15-17h (in A302) Thursdays, 17-19h (in "Large Lecture Theater" Sand 6/7)
Credits	4 hours per week lectures+2 hours per week problem sessions
Start	October 2003
Place	Lectures: Mondays: Sand 1, Raum A301, Wednesdays: Sand 6/7, "Large Lecture Theater"
Turnus	yearly in WS
Exam areas	Applied CS and Bioinformatics
Remarks	Lectures will be held in English

Description:

Core algorithmic problems in bioinformatics.

0. Introduction
1. Probability
2. Pairwise Alignment
3. BLAST, FASTA and BLAT
4. Multiple Alignment
5. RNA secondary structure
6. Protein secondary structure
7. Protein tertiary structure
8. Physical mapping
9. Phylogeny
10. Whole genome phylogeny *
11. Consensus networks *
12. DNA compression *

Download the script here.

*) Diese Kapitel sind nicht prüfungsrelevant. Im Kapitel "Protein secondary structure" steht die Rolle des
"Hydrophobic Moments" im Vordergrund. Im Kapitel "Protein tertiary structure" sollte nur der "Rosetta Algorithm" in Detail besprochen werden.

Assignments:

Assignment1 Java1
Assignment2 Java2
Assignment3 Java3
Assignment4 Java4
Assignment5 Java5
Assignment6    Java6
Assignment7    Java7
Assignment8    Java8
Assignment9    Java9
Assignment10 Java10
Assignment11 Java11
Assignment12 Java12
Assignment13
Assignment14
Assignment15

Requirements:

For students in their 5. semester or higher.

Credits for problem sessions:

To obtain credits for attending the problem sessions, you are required to regularly and actively participate in the problem sessions. Additionally, you must regularly hand in assignment sheets and obtain at least 60 % of all possible assignment points. Students are permitted to work in groups of up to two people per group.
Alternatively, you may hand in work for a group of three people. In this case, 75 % of all points must be attained.

Authorship:

These lectures, script, Java files and assignments were developed at the ZBIT by Daniel Huson. Parts of this material is used in a modified form in bioinformatics courses at the FU Berlin and at Uppsala University.