This page contains the information you will need to complete the assingments in the course. The assignment handouts will be distributed in class, but you may need other files posted here such as DNA sequences, etc. Programming assignments must be submitted electronically through the student account section. Other portions of the assignment may be submitted electronically or by hand at the start of class.
Although there are no plans to teach this class again, the solutions for these assignments have been removed as a courtesy to other instructors. If you would like to view the solutions to a particular assignment, please contact Nick Fitzkee (nickfitzkee (at) jhu (dot) edu).
| Assignment 1 - February 3 | |
| Summary | An assignment testing simple programing and biology concepts. |
| Due Date | Febuary 10, at start of class |
| Handouts |
Assignment 1 Handout (PDF) |
| Files |
for_example.py bubble_sort.py string_example.py string_locator.py string_split.py.py aa_translate.py |
| Solutions |
Written Solutions Question 1c Question 1e Question 1f Question 2b Question 2c Question 2d Question 3c Question 4 |
| Assignment 2 - February 10 | |
| Summary | Python Modules, Library and the DNATools Package |
| Due Date | Febuary 17, at start of class |
| Handouts |
Assignment 2 - Handout (PDF) Assignment 2 - Functions and Modules (PDF) |
| Files |
stattools.py stattest.py dnatools.py dnatest.py |
| Solutions |
Written Solutions Question 2g Question 2l Question 3 |
| Assignment 3 - February 17 | |
| Summary | Sequence Alignment |
| Due Date | Febuary 24, at start of class |
| Handouts |
Assignment 3 - Handout (PDF) |
| Files |
matrix.py needleman.py algebra.py align.py |
| Solutions |
Written Solutions Question 1a Question 1c Question 1d Question 3a |
| Assignment 4 - February 24 | |
| Summary | Using and understanding the BLAST suite of programs |
| Due Date | March 10, at start of class |
| Handouts |
Assignment 4 - Handout (PDF) |
| Files |
seq_a.fasta seq_b.fasta seq_c.fasta |
| Solutions |
Written Solutions |
| Assignment 5 - March 9 | |
| Summary | Gene Expression Analysis (with lab 2) |
| Due Date | March 17, at start of class |
| Handouts |
Assignment 5 - Handout (PDF) |
| Solutions |
Written Solutions Question 3e |
| Assignment 6 - March 16 | |
| Summary | Protein Structure Analysis (with lab 3) |
| Due Date | March 31, at start of class |
| Handouts |
Assignment 6 - Handout (PDF) |
| Files |
rbp_torsions.txt cadist.py hw06_q5.pdb |
| Solutions |
Written Solutions Question 4b (Ramachandran Plot) Question 5a (CA-CA distances) |
| Assignment 7 - March 31 | |
| Summary | Proteomics (with lab 4) |
| Due Date | April 7, at start of class |
| Handouts |
Assignment 7 - Handout (PDF) |
| Files |
hw07_q4a.py test_1.fasta test_2.fasta 1f88.fasta 1f88.pse 1mbo.fasta 1mbo.pse |
| Optional Reading | Wimley, W. C., and White S. H. (1996) “Experimentally determined hydrophobicity scale for proteins at membrane interfaces.” Nature Structural Biology 3 (10): 842-848. [PDF] |
| Solutions |
Written Solutions Question 4a (Hydropathy program) Question 4c (1f88 plot) Question 4d (1mbo plot) |
| Assignment 8 - April 7 | |
| Summary | Multiple Sequence Alignment (with lab 5) |
| Due Date | April 21, at start of class |
| Handouts |
Assignment 8 - Handout (PDF) |
| Files |
hw08_q5.py matrix.py lipocalins.mfasta |
| Solutions |
Written Solutions Question 4e (N Function) Question 5 (PSSM Program) |
| Assignment 9 - April 21 | |
| Summary | Phylogenetic Analysis (with lab 6) |
| Due Date | April 28, at start of class |
| Handouts |
Assignment 9 - Handout (PDF) |
| Files |
artificial.fasta |
| Solutions |
Written Solutions |
| Assignment 10 - April 21 | |
| Summary | The Human Genome Project |
| Due Date | May 5, at start of class |
| Handouts |
Assignment 10 - Handout (PDF) |
| Files |
sequence.fasta |
