Perl IV Problem Set

1. Create a shuffled sequence
	Turn a DNA string into an array with split()
	Use a for loop to perform the following procedure N times (N = length of seq)
		Select a random position A with rand()
		Select a random position B with rand()
		Exchange the letters at array indices A and B
	Print the now shuffled sequence

2a. Start with 2 very similar DNA sequences. 
	Align with ClustalW or some other web alignment application. 
	Output should be in fasta format.
	Store (copy and paste) the sequence, including dashes, from each ClustalW fasta output in a separate string variable inside your script.
	Turn each string into an array with split()
	Use a for loop to compare each index for nucleotide differences.
	Report the nucleotide position of each difference.

2b. Do the same as above but instead of coping and pasting into string variables
import from a file.

3. Calculate GC content
	Turn a DNA string into an array with split()
	Use a foreach loop to look at each nucleotide in turn
	Calculate total length of the sequence
	Keep a running total of C's and G's
	Print the calculated GC content as a percent.


4.  Run this code. Is its output what you expect? Why?
                  for (my $i = 0; $i < 10; $i++) {
                   if ($i = 2) {
                       print "\$i = $i\n";
                   }
                  }