Assignments

Special software is required to use some of the files in this section: .pdb, .mat, and .m.


ASSIGNMENTS SUPPORTING FILES SOLUTIONS
Assignment 1 (PDF) cSNPs.txt (TXT - 4.2 MB) [Human SNP data]

SNPData.mat (MAT) [SNP data in MATLAB® friendly form. To upload in MATLAB®, just type load filename at the MATLAB® prompt.]
(PDF) (Courtesy of Ken Roach. Used with permission.)
Assignment 2 (PDF) parseBLATAlignment.m (M) [MATLAB® function. Use this function on the output of BLAT for each gene to figure out where the human and chimp sequences diverge, and how each change the codons.]

These two text files are examples of how the data for each gene should look like:

F10Human.txt (TXT) [Factor 10 human sequence. This file is the sequence for the coding region of coagulation factor X obtained from NCBI. This is what you BLAT against the chimp genome. Save the output of BLAT in F10Blat.txt.]

F10Blat.txt (TXT) [Factor 10 Blat Output. The F10Blat.txt is given as input to the MATLAB® function that will output the divergent codons between the human and chimp sequences.]
(PDF) (Courtesy of Ken Roach. Used with permission.)
Assignment 3 (PDF) SerProteases_PS3.pdb (PDB) [Overlapped structures of serine proteases.]