my $fasta_example = <<'END_FASTA_EXAMPLE'; >Rosetta_Example_1 THERECANBENOSPACE >Rosetta_Example_2 THERECANBESEVERAL LINESBUTTHEYALLMUST BECONCATENATED END_FASTA_EXAMPLE my $num_newlines = 0; while ( < $fasta_example > ) { if (/\A\>(.*)/) { print "\n" x $num_newlines, $1, ': '; } else { $num_newlines = 1; print; } }