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Algorithms in Bioinformatics I
Lecture: Algorithms in Bioinformatics I
| 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:
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.
