CSE 4425: Introductory Computational Bioinformatics
Winter 2018
General Information
Instructor: Suprakash Datta
Office: Lassonde, room 3043
Telephone: (416) 736-2100 ext. 77875
Lectures: Tue-Thu, 5:30-7:00 pm in CC 106
Office Hours : Tue-Thus, 12:30 - 2pm, or by appointment in
Lassonde 3043
Email: [lastname]@cse.yorku.ca (If possible, consider using your york
account when sending me email.)
News
- Submit the project report using (web)submit using the name "project"
- The extension for assignment 1 is postponed to Oct 19. I want to cover Fourier transforms in class before the assignment is due. Also please submit electronically using submit or websubmit. The directory os called a1.
- Welcome to CSE 4425!
Assignments
- Assignment 1: R Basics
Notes:
- Learn about the sample() and seq() functions
- The read.fasta() method stores the sequence information in a data frame and not a simple array. You can use the getsequence() method to extract the sequence.
- I used the coding region 56863-58062 and the non-coding region 787-3221.
Solutions are in https://www.eecs.yorku.ca/course_archive/2018-19/F/4425/ASSGMTS/a1-sol.pdf
- Assignment 2: Simple exon prediction.
Use the sapply() command for efficiency -- an example is here. A second
example with jumping windows is here.
- Assignment 3: Fourier phase analysis of DNA.
The project details are here.
Lectures
- Lec 1 (Sept 6): General introduction to Bioinformatics. No slides
used.
- Lec 2 (Sept 11): Introduction to Bioinformatics. Chapter 1 slides, Chapter 2 slides.
- Lec 3 (Sept 13): Introduction to Bioinformatics continued. Introduction to R
- Lec 4 (Sept 18): Sequence Alignment. slides.
- Lec 5 (Sept 20): Sequence Alignment continued. slides.
- Lec 6 (Sept 25): Sequence Alignment (Chapter 3 from the book). slides.
- Lec 7 (Sep 27): BLAST (Chapter 4 from the book). slides.
- Lec 8 (Oct 2): Multiple Sequence Alignment (Chapter 6 from the book). slides.
- Lec 9 (Oct 4): Multiple Sequence Alignment slides.
- Lec 10 (Oct 16): Multiple Sequence Alignment.
- Lec 11 (Oct 18): Multiple Sequence Alignment.
- Lec 12 (Oct 25): Phylogenetic trees (Chapter 7 in the book). slides.
- Lec 13 (Oct 30): Phylogenetic trees
- Lec 14 (Nov 1): Sequencing (Chapter 9 in the book). slides.
- Lec 15 (Nov 6): Sequencing
- Lec 16 (Nov 8): Sequencing
- Lec 17 (Nov 13): Proteomics. (Chapter 12 in the book). slides.
- Lec 18 (Nov 15): Protein Structure. (Chapter 13 in the book). slides.
- Lec 19 (Nov 20): Protein Structure. Functional Genomics (Chapter 14 in the book). slides.
- Lec 20 (Nov 22): Protein Structure. Functional Genomics (Chapter 14 in the book). slides.
- Lec 21 (Nov 27): Finish Ch 14. Start the Human Genome (Chapter 20 in the book). slides.
- Lec 22 (Nov 29): Finish Ch 20.
- Lec 23 (Dec 4): Bonus topic: Hidden Markov Models. slides.
.
Resources
Textbook (required)
Bioinformatics and Functional Genomics, 3rd Edition, by Jonathan Pevsner, Published by Wiley, ISBN: 978-1-118-58178-0. Companion
Website.
References
Essential Bioinformatics Jin Xiong, Cambridge Univ. Press, 2006.
Academic Honesty
It is important that you look at the departmental guidelines
on academic honesty. Although you may discuss the general approach to
solving a problem with other people, you should not discuss the solution in
detail. You must not take any written notes away from such a discussion.
Also, you must list on the cover page of your solutions any people with whom
you have discussed the problems. The solutions you hand in should be your
own work. While writing them, you may look at the course textbook and your
own lecture notes but no other outside sources.
Grades
Grades can be checked online on ePost here (you need your CSE login/passwd to access it).
- 3 assignments, 15% total.
- Midterm (25%): Oct 23, in class.
Syllabus: Everything covered in class before the study week.
Sample questions are here.
- Final Exam (35%): scheduled by the registrar:
Syllabus: Everything covered in the course.
Time/date: TBA
- Project: 25%
Important dates
See this page
for the full list.
- Sept 5: First day of class
- Oct 6-12: Reading week
- Nov 9: Last day to drop courses without receiving a grade
- Dec 4: Classes end
- Dec 5: Study day
- Dec 6-21: Exam period
Missed test/exam
If you miss a test or the final due to medical reasons you are required to
contact the instructor within 7 days of the scheduled exam with
documentation. York University has a new form that your doctor should fill
out. You can download it by clicking here.