CS9871 - High Throughput DNA Sequencing

Course description

DNA sequencing is the procedure that determines the order of the nucleotide bases - adenine, guanine, cytosine, and thymine - in a molecule of DNA. Research in biomedical sciences has been revolutionized by the possibility to sequence the molecule of DNA. Great demand for rapid and affordable DNA sequencing caused the replacement of the Sanger sequencing method by improved technologies that can produce huge amounts of data at ever decreasing costs. Fierce competition produced a number of sequencing technologies, including Illumina/Solexa, Roche 454, AB SOLiD, Ion Torent, Pacific Biosciences. These high-throughput technologies enable many fundamental applications, including de novo genome assembly, genome resequencing, cancer mutation discovery, metagenomics, DNA-protein interaction discovery, personalized medicine, etc. The course starts with an introduction to basic concepts of computational molecular biology, including sequence alignment, dynamic programming, BLAST, spaced seeds, suffix trees, suffix arrays, Markov chains and hidden Markov models, profile HMMs for sequence families, multiple sequence alignment methods. In the second half the course will focus on hot topics in DNA sequencing. We will discuss the most important algorithms and software programs for error correction, genome and meta-genome assembly, genome resequencing (read mapping), genomic variation detection, etc.

Prerequisites

CS9871: None.
CS4463: Computer Science 3331A/B and 3340A/B; Biochemistry 2280A is recommended

Instructor

Dr. Lucian Ilie, MC368, e-mail: ilie

csd.uwo.ca

Useful books (not required)

W.J. Ewens, G.R. Grant, Statistical Methods in Bioinformatics, 2nd edition, Springer, New York, 2005.
R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis, Cambridge Univ. Press, 1998 (11th printing, 2006).

Evaluation (tentative):

Participation: 20%
Presentations (given by each student in class): 80%

Presentation schedule

There will be no assignments or exams

Class time

Wednesdays, 11:30am - 1:30pm, MC316

Office hours

Wednesdays, 2:30 - 3:30pm, MC368

Academic Accommodation for Medical Illness

If you are unable to meet a course requirement due to illness or other serious circumstances, you must provide valid medical or other supporting documentation to your Dean's office as soon as possible and contact your instructor immediately. It is the student's responsibility to make alternative arrangements with their instructor once the accommodation has been approved and the instructor has been informed. In the event of a missed final exam, a "Recommendation of Special Examination" form must be obtained from the Dean's Office immediately. For further information please see: http://www.uwo.ca/univsec/handbook/appeals/medical.pdf
A student requiring academic accommodation due to illness should use the Student Medical Certificate when visiting an off-campus medical facility or request a Record's Release Form (located in the Dean's Office) for visits to Student Health Services. The form can be found here: https://studentservices.uwo.ca/secure/medical_document.pdf
Students who are in emotional/mental distress should refer to Mental Health@Western http://www.uwo.ca/uwocom/mentalhealth/ for a complete list of options about how to obtain help.

Accessibility Statement

Please contact the course instructor if you require material in an alternate format or if you require any other arrangements to make this course more accessible to you. You may also wish to contact Services for Students with Disabilities (SSD) at 661-2111 x 82147 for any specific question regarding an accommodation.

Ethical Conduct

Scholastic offences are taken seriously and students are directed to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at the following Web site: http://www.uwo.ca/univsec/handbook/appeals/scholoff.pdf.
Plagiarism: Students must write their essays and assignments in their own words. Whenever students take an idea, or a passage from another author, they must acknowledge their debt both by using quotation marks where appropriate and by proper referencing such as footnotes or citations. Plagiarism is a major academic offence.
If assignments are to be individual assignments: All assignments are individual assignments. You may discuss approaches to problems among yourselves; however, the actual details of the work (assignment coding, answers to concept questions, etc.) must be an individual effort.
The standard departmental penalty for assignments that are judged to be the result of academic dishonesty is, for the student's first offence, a mark of zero for the assignment, with an additional penalty equal to the weight of the assignment also being applied. You are responsible for reading and respecting the Computer Science Department's policy on Scholastic Offences and Rules of Ethical Conduct.
The University of Western Ontario uses software for plagiarism checking. Students may be required to submit their written work and programs in electronic form for plagiarism checking.