Computational Biology (426) Spring 1997

A review of computational methods used for the analysis of DNA and protein sequences. The main emphasis will be on algorithms. Some time will be devoted to study of databases and Internet resources available for computational biology research.



Courses on Internet
Some relevant links
Some general references

Participants


Seminars (tentative)


Date Subject By Main References Software
1 6/2/97
Introduction 
  • Overview
  • Assignment of topics
PW
2 13/2/97
Pairwise sequence alignment
  • Global alignment - dynamic programming algorithm
  • Local alignment and similarity 
  • Heuristics 
LK
3 20/2/97
Multiple sequence alignment
  • Dynamic programming 
  • Carrillo-Lipman method 
  • Heuristics
PW
4 27/2/97
Sequence Assembly
  • Shortest superstring 
  • Hybridization 
PW
  • Blum et al.
5 6/3/97
Physical Mapping
  • PQ-trees 
  • Interval graphs 
CTJ+CJ
  • Alizadeh et al. 
6 13/3/97
Restriction Maps
  • Double digest problem
  • Uncertainty
PW
  • Pevzner
7 20/3/97
Sorting by reversals
  • Exact algorithms
  • Approximations
K+HHS
  • Kececioglu and Sankoff
27/3/97
No Seminar
8 3/4/97
Protein Folding
  • Hydrophobic-hydrophilic model
JDA
  • Hart and Istrail
9 10/4/97
Protein Folding
  • Genetic algorithm 
K+HHS
10 17/4/97
Phylogenetic Trees
  • Perfect phylogenies
HP+JL
  • Agarwala and Fernandez-Baca
  • Applets
11 24/4/97
Phylogenetic Trees
  • Distance-based methods
TA
  • Farach et al.
1/5/97
No Seminar
8/5/97
No Seminar
12 15/5/97
Molecular Computers
BM+BTD
13 22/5/97
Evaluation
PW



Main References

E-mail:
pawel@diku.dk