1. Remove the 'portion' calculations by using the integer product of 'lim' and 'length' in the comparisons. (Eliminates floating point calcuations and comparisons in the loop!)
2. Put the 'tr's in the comparison so that you can short-circuit having to do all the translations.
3. Use 'grep'.
4. Return an array reference from the subroutine.

#!/usr/bin/perl

use strict;
use warnings;

MAIN:
{
    my @set = qw (AAAAAT ATCGAT TTTTTG GCCCCC GTGGGG);
    my $lim = 0.75;

    print("BEFORE: ", scalar(@set), "\n");

    my $results = remove_poly(\@set, $lim);

    print("AFTER:  ", scalar(@$results), "\n");
    #print(join("\n", @$results), "\n");
}

exit(0);

sub remove_poly
{
    my $array = $_[0];
    my $lim   = $_[1];

    $lim = int($lim * length($$array[0]));

    my @results = grep { (($_ =~ tr/A//) <= $lim) &&
                         (($_ =~ tr/T//) <= $lim) &&
                         (($_ =~ tr/C//) <= $lim) &&
                         (($_ =~ tr/G//) <= $lim) }
                    @$array;

    return (\@results);
}

# EOF
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