CS7960 Topics in Bioinformatics
Time: MWF 9:30 AM to 10:20 AM
Place: Old Main 304
Office Hours: MWF 3pm-4pm
Office: Old Main 401F
Instructor: Charles Yan
797-2570
Course Goals:
Learning Outcomes:
o Choose and modify suitable computational models to solve the problem
o Interpret the advantages and/or disadvantages of the approach
Grading:
Late Homework:
Homework is due at midnight on the due date. Homework handed within three days after the due time will be subjected to a 25% reduction in score. Homework overdue by more than three days will get a grade of 0, except for a legitimate reason, e.g. illness, which must be documented.
Homework:
You should finish homework independently. Discussions are encouraged, but copying homework is cheating.
Final Project:
If you wish, you can do the final project in a group that has no more than two students. When doing the project in a group, the contribution of each student must be clearly stated in the report.
Course website:
The website for this course is http://www.cs.usu.edu/~cyan/CS7960/.
Textbook:
Biological sequence analysis By R. Durbin, S. Eddy, A. Krogh and G. Mitchison, Cambridge University Press, ISBN 0-521-62971-3
Bioinformatics: A practical guide to the analysis of genes and proteins. Andreas D. Baxevanis, B.F. Fancis Ouellette. John Wiley & Sons, Inc. ISBN: 0-471-47878-4
Last day to Drop: Jan 28
Last day to Add: Jan 28
Code of Conduct for
Computer Science Classes:
As a computer scientist, or someone taking a computer
science class, you are expected to perform your work at all times in an ethical
manner. This means that in addition to doing your own work and giving
appropriate credit when the work of others is used, you are required to protect
your work.
A student that protects their work will not allow another
student access to that work whether it be allowing it to be copied, or treating
its security in such a way as to give unintentional access, such as
"accidental" loss. It is the policy of the department that when
duplicate (essentially the same) work is turned in by two or more students,
without acknowledgement of allowed cooperation, all involved students will be
considered in violation of this department policy. Under such circumstances,
each student will receive minus the points possible for the work.
Thus, for a 15 point assignment, all would receive -15 points. If the
infraction is deemed more egregious, then further action may be taken.
Students
with physical, sensory, emotional or medical impairments may be eligible for
reasonable accommodations in accordance with the Americans with Disabilities
Act and Section 504 of the Rehabilitation Act of 1973. All accommodations are
coordinated through the Disability Resource Center (DRC) in Room 101 of the
University Inn, 797-2444 voice, 797-0740 TTY, or toll free at 1-800-259-2966.
Please contact the DRC as early in the semester as possible. Alternate format
materials (Braille, large print or digital) are available with advance notice.
3. HMM training
5. Gene finding papers:
5.1 GeneMark, GeneMark_hmm, GeneMarkS, GeneMark_ES
5.2 GENSCAN, GenomeScan
5.3 Glimmer1.0, Glimmer 2.0, GlimmerHmm