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Assignments

MATLAB® software is required to run the .m files in this section. RasMol software is required to run the .pdb files found in this section.  Any number of biological sequence comparison software tools can be used to import the FASTA formatted sequence (.fa) files in this section. Use the Python Interpreter to run the .py files found in this section.

ASSIGNMENTS SUPPORTING FILES
Homework 1 (PDF) prob2seqs.fa (FA)
prob3inputseqs.fa (FA)
prob4seq.txt (TXT)
Sample run for problem 6 (TXT)
Homework 2 (PDF) dino1.fa (FA)
dino2.fa (FA)
pombe.fa (FA)
motifs.txt (TXT)
random.fa (FA)
5primesplicesites.txt (TXT)
3primesplicesites.txt (TXT)
splicing.run (TXT)
motif.run (TXT)
Homework 3 (PDF) 1fxd.pdb (PDB)
rmsd.py (PY)
Homework 4 (PDF) hw4.m (M)
repressilator.m (M)

Repressilator model based on: Elowitz M. B., and S. Leibler "A synthetic oscillatory network of transcriptional regulators." Nature 403, no. 6767 (20 Jan 2000): 335-8.