---

• Overview
  • Main Page
  • History
  • Facts and Figures
  • People
  • Administrative Forms
  • Department Calendar
  • Newsletter
• Research
  • Main Page
  • Faculty
  • Positions
  • Collaborators Needed
  • Funding
  • Publications
• Post-doctoral Scholars
  • Main Page
  • Positions
  • Funding
  • Life in London
  • Postdoctoral Association at Western
  • School of Graduate and Postdoctoral Studies
• Graduate Program
  • Main Page
  • Applications/ Admissions
  • Program Information
  • Seminars
  • Positions
  • Approved Applications (Restricted)
  • Contact
• Undergraduate Program
  • Main Page
  • Courses
  • Honors Project
  • BMSc Program
  • Funding
  • Positions
  • Contact
• Facilities & Services
  • Main Page
  • London Regional Proteomics Centre
  • Peptide Synthesis
  • Oligo Synthesis
  • Other Facilities
  • Outreach Science Ontario
  • Microbiota

 

 

BIOCHEMICAL INFORMATICS

Biochemistry 4445F

COURSE INFORMATION

 

This course teaches the fundamentals of 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 significantly different sequences retain activity in different organisms.

This is a laboratory course that provides hands-on application of the resources using examples drawn from the real world. The internet is a tremendous resourse 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 prodedures upon completing this course:

1. Generate valid Perl programs to manipulate large files
2. Use regular expressions to manipulate sequence data
3. Identify and use the appropriate databases to solve a problem
4. Correctly use the information in sequence annotation
5. Choose the appropriate tools to search the primary and secondary databases for genes of interest.
6. Identify conserved regions in proteins based on their primary structure
7. Perform structural alignments and use this as a guide for multiple sequence alignments
8. Use conserved information to conduct a refined database search.
9. Identify putative genes or other interesting sequences in a defined genomic interval.

LECTURES

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

Course Content

Introduction to the computer lab, unix and text editors. Why study bioinformatics? A TED talk by Juan Enriquez. Annotation: concepts and methods.
Information content in sequences & substitution matrices, The Smith-Waterman algorithm, Database searching with BLAST and FASTA, Data manipulation 1: Patterns
Data manipulation 2 Advanced pattern matching, Multiple Sequence alignment
Assignment on Clustalw, Structure alignment, Structure-based sequence alignment
Phylogeny for Biochemists, Next Generation sequencing and genome assembly.

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 assignment is worth 4 marks, the next eight are worth 8 marks each, the final assignment is worth 32 marks. Each assignment covers a specific topic which is covered in lecture. Please note tha t 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.

If you have academic conflicts with the midterm test dates, inform Melita Hayes in the Biochemistry Office (Room M342, Medical Sciences Building) by email or in writing as early as possible. Written requests for alternate test times will be considered up to one week before the scheduled test. If you have a non-academic conflict with the midterm test dates, consult the Dean's office to determine if accomodation is warranted.

INSTRUCTIONAL INFORMATION

There is not a standard. I recommend Fundamental Concepts of Bioinformatics by Krane & Raynor (2003) or "Introduction to Bioinformatics" by Attwood and Smith (1999) or Bioinformatics by Baxevanis & Ouellette (2000). I have samples available for viewing. There will be other assigned readings from time to time. Students are expected to read the documentation pages for the bioinformatic packages and databases that are used in the course.

---

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

---

Revised July 25, 2011 by Melita Hayes