BIOLOGICAL SEQUENCE ANALYSIS
Math/Stats 547 (Lecture) and 548 (Lab) MWF, 9-10 (1084 East Hall); Fri, 10-11 (B743 East Hall)

 

Syllabus

Assignments

Lab Worksheets

548 Resources

Web Resources

Term Project

Speaker Schedule

Outside Seminars

Contact Instructor

The 548 Laboratory Worksheets:

These are the worksheets for the Winter Term, 2004. For 2003 worksheets, go here.

Link to the PHX Worksite. Deposit data and code here. (Your browser has to be relatively new to do this successfully.)

January 13, 04 Accounts; familiarity with resources
January 16, 04 Accounts; familiarity with resources (necessary repetition of Jan 13, 04)
January 23, 04 NCBI, SwissProt, PDB; coding first example.
January 30, 04 PDB files, Pairwise comparisons, PHX genes, Molecular Viewers.
February 6, 04 Significance of PAM times; PHX data.
February 20, 04 Local fixes for HMM Toolbox and SeqAln; Viterbi, BW/EM training; PHX data collection; testing SeqAln fix.
March 5, 04 Local fixes for HMM Toolbox and SeqAln; BW/EM training; PHX data collection; profile HMMs.
March 12, 04 No worksheet.
March 19, 04 PHX data organization: Worksite available;
finish HMM training example.
March 26, 04 PHX data and code reports;
initial estimates and HMM training example;
Miller-Urey soup and aminoacyl synthases, introduction.
April 2, 04 PHX data and code reports;
Miller-Urey soup and aminoacyl synthases:
data collection and strategy for analysis.
April 16, 04 Summary and evaluations; further literature.
End of Term Procedures.