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BIOCHEMICAL INFORMATICS

Biochemistry 4445F

COURSE INFORMATION

 

This course teaches the fundamentals of sequence alignment, protein family building, genome database searching and data manipulation. Emphasis is placed on the basics of pairwise search methods and on many of the most widely used computer-based sequence comparison resources on the internet. We apply the new-found skills to try and understand the evolution of protein families and how proteins with signicantly dierent sequences retain activity in dierent organisms.

This is hands-on learning course that provides applications of the resources using examples drawn from the real world. The internet is a tremendous resource that contains all the information needed to use it. Wherever possible, we will draw on the original resources and manual pages. Students should be able to understand and perform the following procedures upon completing this course:

1. Identify putative genes or other interesting sequences in a dened genomic interval.
2. Generate valid programs to automate tasks
3. Use regular expressions to manipulate sequence data
4. Identify and use the appropriate databases to solve a problem
5. Generate an appropriate dataset to solve a problem
6. Choose the appropriate tools to search the primary and secondary databases for genes of interest.
7. Correctly annotate protein sequences
8. Identify conserved and covarying regions in proteins based on their primary structure
9. Perform structural and multiple sequence alignments

LECTURES

Wednesday 9:30 - 11:30 AM
2 lecture hours, 3 laboratory hours

ANTIREQUISITES

PREREQUISITES

Biochemistry 3381A.

INSTRUCTORS

Course Manager
Dr. Greg Gloor	MBL C8	519-661-2111 x83526

EVALUATION

There are 13 sessions and 11 assignments. The first 3 assignment are worth 4 marks each, the next eight are worth 8 marks each, the final assignment is worth 24 marks. Each assignment covers a specific topic which is covered in lecture. Please note that the assignments are different than those used in any previous delivery of this course! Students have one week to complete each assignment except the final assignment, which is due the last day of class. There is also a weekly tutorial that is mandatory for all students.

INSTRUCTIONAL INFORMATION

No Textbook. Students are expected to read the documentation pages for the bioinformatic packages and databases that are used in the course. Readings will be assigned prior to class and will be posted on the WWW page.

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Scholastic Discipline
Statement on Academic Offences
University Policy for Plagiarism
Absences from course commitments
Support Services

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Revised September 11, 2012 by Melita Hayes