I used regular expressions here to capture all consecutively appearing upper case alphabets separated by word boundaries (\b). Please check the perl regular expressions documentation

You don't use split ?

You could use split if you like but i think it is better to split by \W+ (non-word character) rather than \s+. This helps keep pattern matching simple in the next step. For the sample text below, using \s+ instead of \W+ would find none unless we perform a more complicated pattern matching later.

my %acronyms;

my $text= "An important class of transcription factors called general 
+transcription factors (GTF) are necessary for transcription to occur.
+ The Most common GTF's are TFIIA, TFIIB, and TFIIE.And a few more not
+ mentioned here.";

my @words = split('\W+', $text);

foreach(@words) {
       if($_ =~ m/^[A-Z]+$/){ $acronyms{$_}++; }
}
foreach( keys(%acronyms) ){ print "$_ seen $acronyms{$_} times\n"; }
[download]