CS 482/682 Winter 2022

Term and Year of Offering: Winter 2022

Course Number and Title: CS482, Computational Techniques in Biological Sequence Analysis.

Lecture Time: Tue. and Thur. 11:30AM - 12:50PM.

Classroom: Online until further notice. MC4042 when classroom teaching is resumed by the university.

Instructor: Bin Ma,

Course Description:

Computer science principles and algorithms in biological sequence analysis. Topics include algorithms for sequence comparison, for large-scale database search in biological databases, for evolutionary tree reconstruction, for identifying important features in DNA and RNA sequences, for protein sequence identification and underlying computational techniques.

Course Objectives:

This course introduces the algorithms and computer science ideas used in understanding biological sequences. Whereas BIOL 365 introduced applications of computational techniques in genome analysis, this course focuses on their underlying algorithmic ideas.

Course Overview:

• Introduction   Brief review of the fundamentals of molecular biology and genetics, in context of biology as an information science.
• Pairwise Sequence Alignment  Classic dynamic programming ideas for pairwise sequence alignment. Statistical measures of alignment significance. Probabilistic models of homologous sequences.
• Heuristic Sequence Alignment  Mathematical ideas underlying BLAST, FASTA and other heuristic sequence aligners. Applications of sequence alignment. Multiple alignment.
• Exact string matching  Suffix trees, suffix arraies, BWT, and their application in pairwise and multiple alignment.
• Protein sequence identification  Mass spectrometry and its application in protein identification and sequencing.
• Sequence annotation Gene finding. Sequence feature detection. Motif finding. Hidden Markov models.
• Evolutionary tree algorithms Classical and contemporary algorithms for inferring evolutionary trees.

Textbooks:

No textbooks. Course notes will be supplied on course website.

Evaluation:

• Four assignments, 60% (15+15+15+15)
• Final exam, 40%.

Assignment late policy:

• No late submission of the assignments will be accepted. Missed assignments will be given a 0-mark. For extenuating circumstances, please see the instructor.

Rules for Group Work:

• Your work must be entirely your own. Looking up a solution in the literature without citing the source is plagiarism and will earn you a mark of -100%; looking up the solution and citing the source will earn you a mark of 0%. Looking up a solution, explaining how it works and why it works, and discussing it will be just fine.
• You are encouraged to work with your classmates on solutions, as long as you provide a list of the people with whom you worked, and as long as your collaborations are at an abstract enough level that your programs and written solutions are products of your own work.
• I may ask students to explain how and why their solutions/codes work on the whiteboard of my office. If you cannot explain them well enough, I will conclude that you have relied on the literature or your classmates too much and will adjust the marks according to my own judgment.

Academic Integrity: In order to maintain a culture of academic integrity, members of the University of Waterloo community are expected to promote honesty, trust, fairness, respect and responsibility. [Check www.uwaterloo.ca/academicintegrity/ for more information.]

Grievance: A student who believes that a decision affecting some aspect of his/her university life has been unfair or unreasonable may have grounds for initiating a grievance. Read Policy 70, Student Petitions and Grievances, Section 4. When in doubt please be certain to contact the department's administrative assistant who will provide further assistance.

Discipline: A student is expected to know what constitutes academic integrity to avoid committing an academic offence, and to take responsibility for his/her actions. A student who is unsure whether an action constitutes an offence, or who needs help in learning how to avoid offences (e.g., plagiarism, cheating) or about 'rules' for group work/collaboration should seek guidance from the course instructor, academic advisor, or the undergraduate Associate Dean. For information on categories of offences and types of penalties, students should refer to Policy 71, Student Discipline, and Guidelines for the Assessment of Penalties .

Appeals: A decision made or penalty imposed under Policy 70 (Student Petitions and Grievances) (other than a petition) or Policy 71 (Student Discipline) may be appealed if there is a ground. A student who believes he/she has a ground for an appeal should refer to Policy 72 (Student Appeals).

Note for Students with Disabilities: The Office for persons with Disabilities (OPD), located in Needles Hall, Room 1132, collaborates with all academic departments to arrange appropriate accommodations for students with disabilities without compromising the academic integrity of the curriculum. If you require academic accommodations to lessen the impact of your disability, please register with the OPD at the beginning of each academic term.