use strict ; use warnings ; my $filename = 'file.fasta'; open my $fh, '<', $filename or die "Could not open file" ; my @chars ; { # Calling local $/ sets the input record separator in this block local $/ = '>' ; while(<$fh>) { chomp ; push @chars, $_ ; } } for ( @chars ) { chomp ; print $_ . "\n" ; }