MBB 841


  • Dr. Fiona Brinkman


  • covers core bioinformatics concepts and tools


  • Extraction of protein names from free text
    • mika04.pdf - Sven Mika, Burkhard Rost: Protein names precisely peeled off free text. ISMB/ECCB (Supplement of Bioinformatics) 2004: 241-247.
    • mbb841-slides-Mika04.pdf - Protein names precisely peeled off free text Presentation

SFU Course Description

Course title: MBB 841-3 Bioinformatics
Section: G01.00
Semester: 2005-3
Instructor: Dr. F.L. Brinkman
Office: SSB 7110
Description/topics: An overview of the newly emerging field of bioinformatics, which is loosely defined as the intersection between the fields of molecular biology and computer science. A combination of lecture format and hands-on instruction is provided in the use of, and theory behind, bioinformatic algorithms/software used in genomic and bioinformatic research. An introduction to the development of bioinformatic software/approaches is included, though only basic computer science and programming knowledge is required for this course.

Course Structure:

The course will comprise a combination of lecture and hands-on tutorial-like sessions. Approximately one week will be devoted to each of the following topics:

1. What is bioinformatics? History of Bioinformatics
2. Biological databases and data models
3. Sequence alignment and searching
4. Sequence alignment and searching: BLAST
5. Gene identification
6. Molecular evolution and multiple sequence alignment
7. Phylogenetic analysis
8. Protein analysis: sequence, domains, secondary structure
9. Protein analysis: 3D structure analysis
10. Bioinformatics standards, programming, and open source developments
11. Current topics in bioinformatics: Microarray analysis
12. Current topics in bioinformatics and future directions

Grading: Lab assignments worth a total of 40% of the final mark will be given and a presentation of a journal article will also be required (40% of mark). One larger lab assignment/project worth 20% of your final mark will be evaluated at the end of term that involves web-based presentation of a series of computational analyses developed that deal with answering a biological question.
Required texts: None.
Recommended texts: A.D. Baxevanis and B.F.F. Ouellette (ed.), Bioinformatics: A practical guide to the analysis of genes and proteins, 2nd Edition. 2001. John Wiley & Sons, USA.
Materials/supplies: None.
Prerequisite/corequisite: Completion of MBB 331 (or BISC 331 or other demonstration of adequate knowledge of genetics), and one introductory computer programming course (e.g. CMPT 101, CMPT 102, CMPT 104, CMPT 110, or equivalent).

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