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Note that the information presented here does not necessarily reflect the most up to date syllabus or course information. Rather this information is intended to provide a general overview of course content from previous offerings.
This course provides an introduction to Bioinformatics and experience with select Bioinformatics tools and databases currently utilized among researchers in Life Sciences. Focus is placed on analysis, storage, and manipulation of genomics and proteomics data. Topics include BLAST, sequence alignment, genome annotation, microarrays, primer design and data storage.
Shakiba Jalal, Computer Science
Email: shakiba@cs.usask.ca
Office: Thorvaldson 178.3
Telephone: 966-6513
Office Hours
Please set up an appointment by emailing the instructor.
Class: Tuesday and Thursday between 11:30 am - 12:50 pm in Arts 108
Lab: Tuesday between 4:30 pm - 5:20 pm in Thorvaldson S311 (in the Spinks Addition)
The prerequisite for BINF 210 is BMSC 200 (or equivalent). It is your responsibility to insure that you have met this requirement. If you don't, and you are registered in Arts & Science, you will not get credit for the course.
The following table provides a tentative schedule of high level topics for the class, and when approximately that topic will be covered.
| Week1 | Introduction to bioinformatics and brief review of biology |
| Week2 | Online Prokaryotic/Eukaryotic nucleotide and protein databases |
| Week3 | Gene annotation and BLAST |
| Week4 | Protein sequence alignment and annotation |
| Week5 | PCR primer design |
| Week6 | Genomics |
| Week7 | Microarrays |
| Week8 | Midterm exam and guest speaker |
| Week9 | Gene expression and biomarkers |
| Week10 | Case studies and site visit |
| Week11 | Phylogeny and functional annotation |
| Week12 | High-throughput analysis and data storage |
| Week13 | High-throughput analysis and data storage continues |
By Jonathan Pevsner Publisher: Wiley-Blackwell; second edition (2009) ISBN-978-0-470-08585-1
By Nello Cristianini (Author), Matthew W. Hahn (Author) Publisher: Cambridge University Press; 1 edition (Jan 15 2007) ISBN-13: 978-0521671910
25% assignments (5% per assignment)
20% midterm
5% class participation - given out to students based on participation in class discussions and activites.
50% final
