Bioinformatics II (ST590C)

11:45 AM - 12:35PM Monday and Wednesday and Friday

Room 461 Riddick Hall

Instructor       Office                      Email                                      Phone
Jeff Thorne   323 Ricks       515-1946

Regarding office hours and meetings:   There will be no standard office hours for this course but please feel free to meet with me when you would like to do so.

Textbook: Durbin R., Eddy S., Krogh A., and Mitchison G.  1999.  Biological sequence analysis: Probabilistic models of proteins and nucleic acids. 368pp.  Cambridge University Press, Cambridge U.K.

Additional readings will be announced.

Course Web page is at

Homework       40%        Assigned sporadically
Participation    30%
Final                 30%        format to be announced

Regarding course goals:  The main purpose of this course is to teach statistical techniques that are important for DNA and protein sequence analysis. As time and class interests permit, issues related to protein tertiary structure and RNA secondary structure will also be covered.

Regarding homework:  Several of the assignments will involve writing short computer programs.  To receive credit for these, you must email the completed assignments to me before the due date.  The email message must include (in separate parts): the computer code, any input files, the command used to compile the code, the command used to run the program, and the output obtained.  If you are unable to complete the assignment, email me the portion that you have been able to complete. I am not likely to check the code myself. I am likely to attempt to compile and run your code using the terminal window of Mac OSX. If I have difficulty with compiling and/or running the code, I am likely to ask for your assistance. You are always welcome to talk with me about the assignments, except that I will refuse to help you debug code.

Regarding academic integrity:  Unless otherwise indicated, students are not to seek help on homework  assignments from other students in the class or from people who are not in the class.

Regarding prerequisites:   ST590A or consent of instructor.

Regarding scheduled reading and homework assignments:   these will be dispersed throughout the semester

Regarding incomplete grades and late assignments:   these are discouraged and must be discussed with the instructor on an individual basis

Regarding other stuff: The instructor enthusiastically endorses all requirements at: