Total Elapsed Time = 0.719999 Seconds
  User+System Time = 0.186597 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 17.1   0.032  0.032   2335   0.0000 0.0000  main::method2
 16.6   0.031  0.031   2335   0.0000 0.0000  main::method3
 8.57   0.016  0.016      2   0.0080 0.0080  main::BEGIN
 0.00   0.000 -0.000      1   0.0000      -  strict::import
 0.00   0.000 -0.000      1   0.0000      -  strict::bits
 0.00   0.000 -0.000      1   0.0000      -  warnings::BEGIN
 0.00   0.000 -0.000      1   0.0000      -  Exporter::import
 0.00   0.000 -0.000      1   0.0000      -  warnings::import
 0.00   0.000 -0.000   2335   0.0000      -  main::method1


##</code><code>##

#! c:\perl\bin
use strict;
use warnings;

my $text="";
my @abstracts=();

open(FH, "pc clean25.txt") or die ("can't");
$text=join("",<FH>);
(@abstracts)=($text=~/<ABSTRACT>(.*?)<\/ABSTRACT>/sg);
foreach my $abstract (@abstracts) {
print "method 1: ",method1($abstract, "prostate"),"method 1: ",method2($abstract, "prostate"),"method 3: ",method3($abstract, "prostate");
}
sub method1 {
my $text=shift;
my $gene=shift;
my $count = () = $text =~ /$gene/g;

return $count;
}

sub method2 {
my $text=shift;
my $gene=shift;
my $count=0;

my $p=0; 
++$count while $p = 1+index( $text, $gene, $p );

return $count;
}

sub method3 {
my $text=shift;
my $gene=shift;
my $count=0;

my $patn = qr/\b$gene\b/;
$count++ while $text =~ /$patn/g; 

return $count
}