Intermediate Perl
GC content is a very interesting property of DNA sequences because it is correlated to repeats and gene deserts. A simple way to calculate GC content is to divide the sum of G and C letters by the total number of nucleotides in the sequence. Let’s assume that you start with a string $sequence.
The WRONG way in which I initially did this was to convert the string to an array of letters, as shown here:
sub calcgc {
my $seq = $_[0];
my @seqarray = split('',$seq);
my $count = 0;
foreach my $base (@seqarray) {
$count++ if $base =~ /[G|C]/i;
}
my $len = $#seqarray+1;
my $num=$count / $len;
my ($dec)=$num =~ /(\S{6})/;
return $dec;
}
This is a very inefficient way of calculating the GC content, because arrays in Perl are quite expensive in terms of memory. The result of this was that I run out of memory quite quickly.
I found a more efficient approach by using the substr function, looping through the whole sequence, taking one base at a time:
sub calcgc {
my $seq = $_[0];
my $count = 0;
my $len = length($seq);
for (my $i = 1;$i<$len+1; $i++) {
my $base = substr $seq, $i, 1;
$count++ if $base =~ /[G|C]/i;
}
my $num=$count / $len;
my ($dec)=$num =~ /(\S{6})/;
return $dec;
}
Now I do not run out of memory and the script promptly calculates the GC content for every sequence I have tried it with. I have not tried it with a whole genome though!
Happy coding!
Filed under: Bioinformatics, Tutorials , array, GC content, perl, substr
Array-CGH can be used to detect whether a patient has a region of the genome missing or duplicated. Probes attached to the chip emit a different color depending on their state of binding. Once the array is washed, most of probe spots will appear yellow, that is, all different probes of the reference genome are bound to the patient’s DNA. If a DNA region is missing in the patient, the complementary spots in the array appear in red. These changes appear in sequential order mapping to the reference genome missing in the patient. Depending on the genes that overlap to the deletion, different symptoms may appear in the patient.
