For this assignment you will turn in:
In class(10pts):
1. A statement of the problem (typed)
2. An explanation of your solution (typed)
3. A flowchart (hand-drawn or computer generated)
4. Pseudocode (typed)
Via BlackBoard(40pts):
1. C program named <username_gc.c
Assignment:
Follow the steps that we have outlined in class for algorithm development to generate a program that reads in DNA sequences from a file and determines the content of A, T, C, and G in the sequence. Specifically, I am interested in the GC content (the percentage of the sequence that it G or C). The first line of the file will be in integer that tells you how many sequences there are in the file. Each line following will contain a single sequence. You will need to store the percent of A, T, C, G in a 2D array, this is because you need to know the average GC content of the genome to determine whether a bacterial gene is, or is not, pathogenic. If a bacterial gene has a higher GC content than the genome as a whole, then it is likely that that gene is pathogenic.
The Wikipedia page on GC content gives additional explanation: https://en.wikipedia.org/wiki/GC-content
Specifications:
Inputs:
- File called sequences.txt (contains a plasmid of Yersina pestis) Outputs:
- File called content.txt containing A, T, C, G, and GC content of each sequence along with a pathogenicity prediction:
EX:
%A
%T
%C
%G
%GC
pathogenic?
10
20
40
30
70
Y
20
50
10
20
30
N
Functions:
1. void printToFile(int seq, float content[seq][4], float avgGC)
a. prints the results out to a file
b. You should open and close your file in this function
2. float averageGC(int seq, float content[seq][4])
a. calculates the average GC content for the whole genome
3. char isPathogenic(float avgGC, float seqGC)
a. returns Y if pathogenic, N if not
* This is the minimum functions that you must use. You may use others if you like.
Other:
1. This is individual work. You may NOT work in groups.
2. Please staple all work together.
3. You are expected to error check.
4. For code: No compile = No points, no exceptions!
5. You must use the functions exactly as described
6. You must have your input file called “sequences.txt” and output file called
“content.txt”
