Protein structure analysis from DNA sequences is an important and fast growing area in both computer science and biochemistry. Although interesting approaches have been studied, it is very difficult to capture the characteristics of protein, since even a simple protein are made of more than 100 amino acids, which makes biochemical experiments very difficult to detect functional components. For this reason, almost all the problems in this field are left unsolved and it is very important to develop a system which assists researchers on molecular biology to remove the difficulties caused by combinatorial ezplasions. In this paper we report a system, called MOLA-MOLA (Molecular biological data-analyzer and Molecular biological knowledge acquisition tool), which eztracts knowledge from amino-acid sequences by controlling application of domain knowledge automatically. We apply this method to comparative analysis of lysozyme and ctlactalbumin. The results show that we obtain several interesting results from amino-acid sequences, which have not been reported before.