Time and Location:  50435R           2:00-4:00 Tue                     Room: SCI-257         

Instructors

Text: No required text book. handouts will be given during the classes.

COURSE CONTENTS: Biological web resources, sequence alignment, BLAST,  phylogenetic trees, sequence assembly, gene recognition, RNA and protein structure, introduction to R, motif identification, microarray analysis, hidden Markov models (HMM). 

Homework: Homework projects will be assigned by the instructors. You should hand in your projects by the due date specified by the instructors.  Points will be subtracted for projects submitted after the due date. 

Grade: Course grade will be based on the homework projects.

Course Webpage:  http://www.cmb.usc.edu/~fsun/Math577/syllabus.htm

 

Tentative Schedule:
 

01/11 1. Introduction to NCBI web resources (Sun) Problem set 1 (Due Date: Feb. 1st)

01/18 2. Introduction to Genome Browser (Sun)

01/25 3. Pairwise and Multiple Sequence Alignment (Sun)

02/01  4. BLAST (Sun) Problem_set_2 (Due Date: Feb. 15th)

02/08  5. Phylogeny (Sun) 

02/15  6. Coalescence (Sun)

02/22 7.  Introduction to Perl (Chen)

03/01 8.  Introduction to Perl  (Chen)

03/08 9.  Gene Finding (Chen)

        03/15 10. Spring break

03/22 11. Structure (Chen) 

        03/29 12. R Intro ( Peter Calabrese) 

        04/05 13. R Practice (Motif finding) and TRANSFAC (Zhou)

        04/12 14.  Clustering (Zhou)

        04/19 15.  Microarray I (Zhou)

        04/26 16. Microarray II  (Zhou)