use Bio::DB::Fasta;


my $db = new Bio::DB::Fasta("Library.fa");

open(INPUT1, "Library.fa") or die "Cannot open Hprot.fa";
open(INPUT2, "Name.fa") or die "Cannot open Hprot.fa";
open(output, ">result.fa"); 

my(@lines1) = <INPUT1>;
my(@lines2) = <INPUT2>;

while $lines1 eq $lines2 && =~ /^Contig*/