my $file = 'test.txt';

{
   local $/ = "\n>"; # eignet sich gut bei FASTA-Sequenzen
   open(my $fh,"<",$file) or die $!;
   while(my $line = <$fh>){
      print "LINE: $line LINEEND\n";
      chomp $line;
      print "LINE: $line LINEEND\n";
   }
   close $fh;
}