Lecturer	Prof. Dr. Daniel Huson and Dr. Christoph Dieterich
Assistants	Tobias Dezulian and Christian Rausch
Office hours	DH: Mondays 16-17h30, office C310a, Sand 14 CD: by appointment TD & CR: Mondays 16-17h30, office C310a, Sand 14
Time	Monday 10:20-12 h, Wednesday 11:15-13 h
Place	A301, Sand 1
Start	Mon., October 16, 2006
Credits	8 LP, 4+2 SWS
Turnus	yearly in WS
Module	Diploma: Applied CS and Bioinformatics; MSc Bioinformatik: Modul Bioinformatik I; MSc Informatik: Wahlfplichtmodul Praktische Informatik
Remark	Lectures will be held in English

Description:

Core algorithmic problems in bioinformatics, including alignment, RNA and protein structure, genome comparison.

Schedule and Script:

This is a tentative schedule and the precise dates of topics might shift slightly depending on the progress made.

16.10.2006	0. Red Tape 1. Introduction 2. Probability
18.10.2006	3. Compression *
23.10.2006	4. Pairwise Alignment (script) (slides)
25.10.2006	continued
30.10.2006	continued
1.11.2006	holiday
6.11.2006	5. BLAST (script) (slides)
8.11.2006	6. Multiple Alignment (script)
13.11.2006	continued (script)
15.11.2006	continued (script)
20.11.2006	continued (script)
22.11.2006	continued (script)
27.11.2006	7. Genome Comparison: Rearrangements (slides) *
29.11.2006	continued: Rearrangements, A-Bruijn Alignment (slides) *
4.12.2006	8. RNA Secondary Structure (script)
6.12.2006	continued (script)
11.12.2006	9. Protein Secondary Structure (script)
13.12.2006	continued (script)
18.12.2006	mid-term exam
20.12.2006	continued (script)
Christmas break
8.1.2007	10. Protein Tertiary Structure (script)
10.1.2007	continued (script)
15.1.2007	11. Phylogeny (script)
17.1.2007	continued (script)
22.1.2007	continued (script)
24.1.2007	continued (script)
29.1.2007	continued (script)
31.1.2007	continued (script)
5.2.2007	continued (script)
7.2.2007	12. HMMs (script)
12.2.2007	final exam
14.2.2007	continued (script)

Oral exams for Diploma students: Topics marked * will not be part of the oral exam.

Assignments:

Assignment 1
Assignment 2
Assignment 3
Assignment 4 Java class ExternalWrapper
Assignment 5
Assignment 6 Java6
Assignment 7
Assignment 8 Java8
Assignment 9 (exam preparation)
Assignment 10 executable Jar, including sources and classes
Assignment 11
Assignment 12 Java 12
Assignment 13 Java 13
Assignment 14 Java 14
Assignment 15 Java&Data 15

Requirements:

For Diplom students in their 5. semester or higher.
For Master students in their 1. semester.

Credits for this course:

Diploma students: To obtain a "Schein" for this course, 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.
Further, you must participate in both exams (mid-term and final) and, in total, obtain at least 30% of all points.

Master students: You must qualify for a "Schein" as described for Diploma students. Your final grade for this course
will be computed as the average grade obtained in the two exams.