Algorithms for Bioinformatics (CPSC 445)

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   Tue+Thu, 9:30-11:00 in
DMP 301
   First class: Tue, 2006/01/10

   Holger H. Hoos
   Office: ICICS/CS complex, Room X542
   Office hours: Tue, 11:00-11:30 + Thu, 12:00-12:30

Teaching Assistants:
   Baharak Rastegari (baharak "at"
   MohammadAli Safari (safari "at"

Course Description:

Bioinformatics involves the application of computational methods in order to address problems in molecular biology. This course will provide a introduction to algorithms and their applications in bioinformatics. Topics in molecular biology that will motivate the algorithmic content of the course include: sequence alignment, phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence annotation, gene expression, and biomolecular computing.

Graduate and senior undergraduate students in computer science, or from the biological sciences who already have a substantial background in programming and algorithm design, are welcome to take CPSC 445. Because the course involves a significant project, a solid background in computer programming is required. Background in discrete mathematics or in probability theory, such as can be obtained in a college level course in Mathematics or Statistics, is especially relevant to the course content. Students should also be comfortable with mathematical reasoning. Solid basic knowledge in molcular biology is required or will need to be ackquired during the course.

Note to students: Due to the interdisciplinary and advanced nature of the material covered, you should expect the course to be very challenging and time-consuming. It will probably involve more work per credit than most other courses you have taken.

Class assignments will familiarise students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. Some assignments will involve the use and extension of software tools, and others will involve written studies of algorithms and their analysis. Class projects will bring together students with different backgrounds to apply ideas from the course to a problem in molecular biology. Students in CPSC 445, the undergraduate version of the course, will work on smaller projects or project components and get additional homework assignments.

Course Outline

A course outline can be found here.

Student Evaluation and Grading

Final grades will be determined approximately as follows: Policy on late assignments and missed course work:




last update 06/04/15, hh