You could always join your @numbers file into one big regex. That way you don't have to slurp @file into memory. I have a feeling it may be huge.

use strict;
open NUMBERFILE, "<\@numbers" or die $!;
my $regex = join "|", map {chomp; "^\\>gb\\|" . quotemeta($_) . "\$"} 
+<NUMBERFILE>;
close NUMBERFILE;
open DATAFILE, "<\@file" or die $!;
my $flag = 0;
while (<DATAFILE>) {
    if (substr($_,0,1) eq ">") {
        $flag = /$regex/;
    }
    print if $flag;
}
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