1MB304: Discrete structures for bioinformatics II 2007

  
   
  • Book: An introduction to bioinformatics algorithms, Jones and Pevzner, ISBN 0-262-10106-8.
  • Credit points: 5 (4 points: Exam, 1 point: hand-ins/project)
  • Lectures (Torgeir R. Hvidsten + guest lecturer)
  • Obligatory hand-in exercises (4 of 6 exercises must be returned and approved)
  • One obligatory computer project (students may work in pairs)
  • There will be a bonus point on the exam for each approved exercise handed in within the deadline (i.e. within one week) and up to four bonus points if the project is approved and handed in within the deadline. Thus there will be a maximum of 10 bonus points amounting to 10% of the exam.
The course teaches computational methods for some of the core applications of bioinformatics :
  • Sequence analysis
    • Sequence motif finding
    • Genome assembly
    • Genome rearrangements
    • Multiple alignments
    • Gene finding
    • ...
  • Ongoing research at the Linnaeus Centre for Bioinformatics
    • RNA folding
    • Protein structure prediction
  Student evaluations: 2006, 2007  
         

When/where?

Topics

Material

  
       
2007.08.27
Monday
10.00-12.00
D1:411, BMC
  • Presentation of the course, the book, the exercises and the computer project.
  • Introduction to discrete structures in bioinformatics (discrete structures, algorithms, recursion, algorithm design, pseudo-code, algorithm complexity, biological problems, bioinformatics)
 Slides
Chapter

2		  
2007.08.28
Tuesday
13.00-15.00
D1:411, BMC
  • Exhaustive search
  • Application: restriction mapping, finding regulatory motifs in DNA sequences
 Slides
Chapter 4		  
2006.08.31
Friday
13.00-15.00
D1:411, BMC		 Exercise: Algorithms, complexity and exhaustive search Exercise 1  
2007.09.03
Monday
13.00-15.00
C8:305, BMC
  • Greedy algorithms
  • Application: genome rearrangements, finding regulatory motifs in DNA sequences
 Slides
Chapter 5 		 
2007.09.04
Tuesday
13.00-15.00
A9:01, BMC 		Exercise: Greedy algorithms Exercise 2  
2007.09.06
Thursday
10.00-12.00
D1:415, BMC
  • Dynamic programming
  • Sequence alignments (global, local, gaps, multiple alignments)
  • Application: gene prediction, BLAST
 Slides
Chapter 6.1-6.13, 7.3, 7.4 and 9.8		  
2007.09.11
Tuesday
10.00-12.00
D1:411, BMC		 Exercise: Dynamic programming Exercise 3  
2007.09.12
Wednesday
10.00-12.00
D1:415, BMC
  • Hidden Markov models
  • Application: Modeling multiple alignments, Pfam
 Slides
Chapter 11		  
2007.09.14
Friday
13.00-15.00
D1:419, BMC		 Exercise: Hidden Markov models Exercise 4  
2007.09.18
Tuesday
13.00-15.00
D1:419, BMC
  • More on hidden Markov models
  • Randomized algorithms
  • Application: Motif finding
 Slides
Chapter 11, 12.1-12.2		  
2007.09.21
Friday
10.00-12.00
A11:0, BMC		 Exercise: Hidden Markov models Exercise 5
Matlab HMM library		  
2007.09.25
Tuesday
08.00-10.00
D5:206b, BMC		 Slides and lecture notes
Research article pp. 631-643 (paper version)		  
2007.09.27
Thursday
13.00-15.00
D1:419, BMC		 Exercise: RNA folding Exercise 6  
2007.09.28
Friday
10.00-12.00
D1:415, BMC
  • Protein structure prediction from sequence
  • Introduction to the computer project: predicting local structure from sequence
  • Summary of the course material
 Slides
Research article 		 
2007.10.02
Tuesday
10.00-12.00
A11:0, BMC		 Computer project Project description
Material 		 
2007.10.03
Wednesday
10.00-12.00
A11:0, BMC 		Computer project    
2006.10.04
Thursday
10.00-12.00
A11:0, BMC		 Computer project    
2007.10.10
Wednesday
13.00-15.00
A11:0, BMC		 Computer project    
2007.10.12
Friday
11.00-13.00
A11:0, BMC 		Computer project
Course evaluation!		    
2007.10.16
Tuesday
10.00-12.00
D1:419, BMC

Questions

Deadline for handing in the computer project report!

    
2007.10.19
Friday
09.00-14.00
B10:1, BMC

Exam

 Relevant previous exams:
2006 (solutions)