local $/ = "\n>"; my %seqs_hash; while (my $line = ) { chomp $line; $line =~ s/^\>?\s*(.+)+$\r?\n// or do { warn "Malformatted sequence\n"; next; }; $seq_name = $1; $line =~ s/\s//gs; $seqs_hash{$seq_name} = $line; }