CS7960 Topics in Bioinformatics

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

Charles.Yan@usu.edu

797-2570

Course Goals:

Become familiar with various bioinformatics problems
Master the computational techniques for biological sequence analysis
Understand the latest advances in bioinformatics

Learning Outcomes:

Set a solid background in bioinformatics
For a given biological sequence analysis problem, students should be able to

o Choose and modify suitable computational models to solve the problem

o Interpret the advantages and/or disadvantages of the approach

Be able to identify and pursue research topics in bioinformatics

Grading:

Homework 75%
Final project 25%

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 26

Last day to Add: Jan 26

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.

Disability Resource Center:

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.

1. Markov Chains

2. Hidden Markov Models

3. HMM training

4. HMM papers: 1, 2, 3

5. Gene finding papers:

5.1 GeneMark, GeneMark_hmm, GeneMarkS, GeneMark_ES

5.2 GENSCAN, GenomeScan

5.3 Glimmer1.0, Glimmer 2.0, GlimmerHmm

6. Gene finding (1, 2, 3):

7. Gene expression analysis

Assignment 1

Assignment 2