Algorithms in Bioinformatics
Teaching Winter Semester 2003/04 Alg. in Bioinformatics I
 
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ZBIT
CS Dept.
University
 

        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:

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.


University of Tübingen