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Algorithms in Bioinformatics I
Lecture: Algorithms in Bioinformatics I
| 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 1Assignment 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 classesAssignment 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.
