You could try replacing

   $count++ while $text =~ /$gene/g; # Count number of instances
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$count = () = $text =~ /$gene/g;
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It may run a little quicker. You could also try

my $p=0; 
++$count while $p = 1+index( $text, $gene, $p );
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Which may be quicker still.

If your process takes a long time to run, the obvious thing to do to save having to wait for the whole thing to complete before you can get a feel for which is quickest would be too use a small subset of the data whilst testing. If the text being search comes from a file, try using head to grab the first couple of hundred lines of the real data and use that for performance testing the options.