Protein structure analysis from DNA sequences is an important and fast growing area in both computer science and biochemistry. One of the most important problems is that two proteins, both of which have the similar three-dimensional structure, have diffe-ent functions, such as ll/sozyme and lactalbumin. In such cases, comparative analysis of both amino acid sequences is effective to detect the functional and structural differences. In this paper, we introduce a system, rolled MWI.5 (Molecular biologists’ Workbench version 1.5), which eJztracts differential knowledge from amino-acid sequences by using rough-set based classification, statistical analysis and change of representation. This method is applied to the following two domain: comparative analysis of lysozyme and a-lactalbumin, and analysis of immunoglobulin structure. The results show that several interesting results from amino-acid sequences, are obtained which have not been reported before.