In this paper, we present an approach based on Burrows-Wheeler transform to compare the protein sequences. The strings representing amino acid sequences do not reflect the chemical physical properties better, and it is very hard to extract any key features by reading these long character strings directly. The use of the Burrows-Wheeler similarity distribution needs a suitable representation which can reflect some interesting properties of the proteins. For the comparison of the primary protein sequences we convert the protein sequences into digital codes by the Ponnuswamy hydrophobicity index, and for the comparison of the structure of the proteins we adjust the topology of protein structure strings, which are simple but useful representation of the secondary structure of proteins to match the Burrows-Wheeler similarity distribution. At last, some experiments show that the approach proposed in this paper is a powerful and useful tool for the comparison of proteins.