Algorithms for Bioinformatics (CPSC 445)

[General Info] · [Course Outline] · [Grading] · [Assignments] · [Resources] · [Course Wiki]
Latest news (2012/04/13):

   Tue+Thu, 14:00-15:30 in
DMP 201
   First class: Thu, 2012/01/05

   Holger H. Hoos
   E-mail: hoos "at"
   Office: ICICS/CS complex, Room X541
   Office hour: Wed, 9:00-10:00
   If I'm not in my office, check ICCS X530.

Teaching Assistant:
   Joel Ferstay (joelaf "at"
   Office: ICCS X468.
   Office hours: Mon, 10:00-12:00

About this course:

Bioinformatics involves the application of computational methods to answer or provide insight on questions in molecular biology. This course provides an introduction to the design and analysis of algorithms for bioinformatics applications. Topics covered will include sequence alignment, phylogenetic tree reconstruction (parsimony and distance-based methods), prediction of RNA and protein structure, gene finding, and motif finding. Algorithmic techniques that will be discussed include dynamic programming and heuristic search methods, as well as combinatorial algorithms for exploration of graphs and trees. Statistical models of molecular sequence and structure, such as hidden Markov models and stochastic context free grammars, and associated algorithms, will also be covered.


CPSC 320 and six credits of BIOL beyond BIOL 111, or equivalent. Experience with design and analysis of algorithms is essential for this course. Related texts listed below, such as “Molecular Biology of the Cell”, will be useful for those who need to catch up on biological background. The algorithms texts by Cormen et al. and by Kleinberg and Tardos provide useful background on combinatorial algorithms, including graph algorithms and dynamic programming algorithms. The text by Hoos and Stützle is a more advanced text which provides very useful background on local search techniques.

Recommended Textbook:

Durbin, Eddy, Krogh, Mitchison: Biological Sequence Analysis. Cambridge University Press, 1998

Course Wiki

You can access the course wiki here: Course Wiki

Student Evaluation and Grading

Final grades will be determined approximately as follows:

Missed Course Work and Academic Misconduct:


  • Assignment 1 (due Fri, 2012/02/17)
  • Assignment 2 (due Tue, 2012/03/27)
  • Assignment 3 (due Tue, 2012/04/03)
  • Assignment 4 (due Tue, 2012/04/10)





    last update 12/04/10, hh