Abstract: We developed a computational method to analyse a coding sequence considering all the information available for the sequence itself and its product. By a graphical analysis of the composition of the nucleic acid sequence, the corresponding amino acid sequence, its chemico-physical properties, the structural and functional information derived from the Swissprot database, the prediction of secondary structure derived from a consensus of five different predictive methods and the three-dimensional information derived from the DSSP program (when the experimental structure of the protein exists), it is possible to investigate and summarize the structural features of a protein from its coding sequence to its structure. The software allows the analysis of multiple alignments of sequences too. In this case, it is possible to perform a deeper analysis to infer on both functional an evolutionary information. Integrating the software with a tool which calculates the substitution rate for both synonymous and nonsynonymous positions , we defined different compositional and substituting behaviour for the secondary structures of 34 mammal coding sequences .