Bioinformatics 210 Detailed Information

Overview

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.

Instructor

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.

Logistics

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)

Prerequisites

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.

Syllabus

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

Textbooks

Two textbooks are recommended, but none are required.
Bioinformatics and Functional Genomics

By Jonathan Pevsner Publisher: Wiley-Blackwell; second edition (2009) ISBN-978-0-470-08585-1

Introduction to Computational Genomics: A Case Studies Approach (Paperback)

By Nello Cristianini (Author), Matthew W. Hahn (Author) Publisher: Cambridge University Press; 1 edition (Jan 15 2007) ISBN-13: 978-0521671910

Grades

25% assignments (5% per assignment)

20% midterm

5% class participation - given out to students based on participation in class discussions and activites.

50% final