Homework 6
Due Wednesday, May 20, at the beginning of class. Homework turned in more than five minutes after the start of class will be marked as late and penalized 10% per day thereafter.
- (5 points) Compute the activation scores at the next iteration for the following protein similarity network. The double-circled node is the query. Use alpha=0.95.
- (2 points) Write down the list of y-ions produced by this peptide: EAMPK.
- (3 points) Use graph plotting software (e.g., Excel) and the following list of amino acid masses to make a plot of the theoretical spectrum produced by the peptide KPLNFR. Include the b- and y-ions, but no flanking peaks or neutral losses.
- (5 points) Following are lists of target and decoy scores. What is the q-value associated with a score of 3.256?
- (5 points) Compute ProteinProphet protein probabilities for the following network. Show your work.
- (5 points) Compute ProteinProphet edge weights for the following network. Show your work.
- (10 points) Write a Python program to read in a network represented as an edge list and compute the average out-degree. Turn in your program as well as the output of the following command:
-
(15 points) Write a Python program to read in a list of target scores
and decoy scores and compute the corresponding q-values. The output
should be a list of target scores in reverse sorted (i.e., highest
score first) order, each with the associated q-value. Turn in your
program and the first ten lines of output produced when you run this
command line:
> python compute-q-value.py target.txt decoy.txt
A 71.03711 E 129.04259 L 113.08406 S 87.03203 R 156.10111 Q 128.05858 K 128.09496 T 101.04768 N 114.04293 G 57.02146 M 131.04049 W 186.07931 D 115.02694 H 137.05891 F 147.06841 Y 163.06333 C 103.00919 I 113.08406 P 97.05276 V 99.06841
Target Decoy 4.447 3.433 3.914 3.371 3.442 3.089 3.256 2.437 3.145 2.043 2.359 1.743 2.330 1.433 2.130 1.224 2.090 1.045 2.001 0.987 1.987 0.903
> python compute-out-degree-edges.py edgelist.txt