Regional variation and function of nucleotide and amino acid sequence

Two methods of qualitative analysis of sequence distribution in DNA and protein are presented. The first method is based on the finding that the frequency of occurrence of each nucleotide in a defined sequence with functional significance more or less deviates from uniform distribution. The deviation found in this defined sequence seems to parallel the function of this sequence. In the second method, two model compounds (trypsin and its inhibitor) have been used to see the topological fit between their local structures. Acrophilicity parameter for amino acid was used to construct the topological structure. Both methods may find practical application in algorithms to design functional DNA and protein molecules.