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 Fall Term, 2005.

For 2004 worksheets, go here.

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.)

Sept 19, 05 NCBI Resourcees, Two Examples.
Sept 26, 05 SwissProt and PDB Resources; BLAST; Perl.
Oct 3, 05 Cn3D (first try at 3D visualization), Predicted Highly eXpressed genes; Perl pseudocode.
Oct 10, 05

Viterbi and EM algorithms, p-value comparisons.

Oct 17, 05 No Meeting: Fall Break.
Oct 24, 05 Clustal, Pfam Database, hmmbuild, and PHX data(1).
Oct 31, 05 HMMer: hmmalign and hmmsearch. PHX data. PHYLIP: examine website.
Nov 7, 05 More HMMs. First phylogeny problems.
Nov 14, 05 No worksheet.
Nov 21, 05 PHX data organization: Worksite available;
finish HMM training example.
Nov 28, 05 PHX data and code reports;
initial estimates and HMM training example;
Miller-Urey soup and aminoacyl synthases, introduction.
Dec 5, 05 PHX data and code reports;
Miller-Urey soup and aminoacyl synthases:
data collection and strategy for analysis.
Dec 12, 05 Summary and End of Term Procedures.