MICa 8006 Homework 2

MICa 8006

Protein Sequence Analysis

Homework 2

Due before class, Tuesday, September 19, 2006

Part A (5 pts) GCG

Use the file test1.pep (in fasta format) on the class website for this part of the assignment. The GCG modules indicated with * produce graphic output. Rename the graphics file (graphics.png) to something meaningful (mv graphics.png newfilename), FTP the file to your computer, and view/print it using a web browser or graphics viewing program. When using the GCG modules indicated, use default values for any changeable parameters.

Convert test1.pep to GCG format (fromfasta); determine its amino acid composition using composition and peptidesort.
Determine other things (peptidestructure/plotstructure*)
The peptidestructure module, among other things, predicts protein secondary structure. Plotstructure displays this in graphical format. Examine the printed output from peptidestructure and plotstructure. Manually draw circles around all regions of predicted alpha helix.
Search for amphipathic helices (helicalwheel*)
Use the start and stop residues for one of the predicted alpha helical regions each time you run helicalwheel. Run helicalwheel one or more times. DO NOT use the entire sequence. On each printout of the output from helicalwheel, write whether, based on this output, the predicted helix is predicted to be amphipathic, and why or why not.

Submit: Copies of the output for peptidestructure and plotstructure, with your manually drawn circles around predicted alpha helices. Copies of each of your runs of helicalwheel, with your written statement on whether the helix is predicted to be amphipathic, and why or why not. No credit without justification.

Part B (5 pts) Perl

Based on the Pseudocode for HW2B, write a Perl program, with comments, that 1) creates three arrays, one with single-letter amino acid codes, one with amino acid names, the third with three-letter codes; 2) randomly chooses an amino acid; 3) randomly prints its single-letter letter code, name, or three-letter code; 4) requests the user to input the other two items; 5) requests that the user draw the chemical structure of the R group of the amino acid, and prints four blank lines so the user has space to do so. The program should repeatedly do this until the user requests it to end. It should produce different random values each time it is run.

Submit: a printed copy of your program and the output it produces when it is run three times, with three or more loops each time. On the printed output, manually draw 2-D structures of the requested R groups.

Part C (10 pts) Perl

Based on the Pseudocode for HW2C, add to the Perl program in Part B (and its comments), so it 1) checks the accuracy of the information input by the user, except for the R group structure; 2) praises correct answers and corrects incorrect answers; 3) counts the correct and the total number of questions; and, when the user requests it to end, 4) reports the percent correct and the date and time.

Submit: a printed copy of your program and the output it produces when run three times as described below, with three or more loops each time. One run should have all answers correct; one run all answers incorrect; and one run a mixture of correct and incorrect answers. Again, draw correct R groups on the printed output.

February 21, 2008 Lynda Ellis

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