Dear PerlMonks,

I am a beginner in perl programming. I am getting wrong result in counting a regular expression from my program. I have given the program below. Can you help me to sort out this problem?

#!usr/bin/perl-w
@k = ‘CCATGNNNTAACCNNATGNNTAGCC’;
$k = join( '', @k);
# Remove whitespace
$k=~ s/\s//g; 
# Count number of bases & regular expressions 
$b=length($k);
print "\n Number of bases (including N): $b.\n"; 
# Count number of A and regular expression (i.e. gene)
$A=0; $GENE=0; 
while($k=~ /A/ig){$A++}
while($k=~ /[AG]TG.*T[AG][AG]/ig){$GENE++}
print "\n A= $A; GENE(S)= $GENE; \n\n"; 
exit;

[download]

I have got the following wrong result:

Number of bases (including N): 25.

A= 5; GENE(S)= 1;

But correct result should be:

Number of bases (including N): 25.

A= 5; GENE(S)= 2;

Actually the value of GENE(S) should be 2 as there are two such regular expressions (sequences) in the array @DNA. Please suggest me the corrections in the code.

In reply to How to get the correct count by supriyoch_2008

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