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 worksheets are from 2003, if not otherwise indicated. They will be updated as the W '04 Term progresses. In the meantime, I leave them and the linked lab worksheets available for the general information of 2004 students.]

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.

March 4, 2003 Making profile HMM's; editing MSA's.
March 11 Fused actin-HSP HMM; first phylogeny exercises.
March 18 Outliers in phylogeny trees; tRNA synthetase Project.
March 25 tRNA-synthetase: complete the alignment. Class I and II .
April 1 tRNA synthetases: family groupings; across species.
April 8 Codon Usage Bias/PHX Data Collection. (Hard Copy Not Available)
April 15 TrpB-synthase across species, and the chronology of amino acids.
End of Term Procedures.