Proteomics is a dynamic property closely related to the conformational mechanisms of protein structure in its physiological environment. To understand and control the function of target proteins, it becomes increasingly important to develop methods and tools for predicting collective motions at the molecular level. In this paper various Bioinformatics tools are used for the primary and secondary structure analysis for HPV Type 16 E7 protein expressed in cervical cancer. ProtPram computed parameters include molecular weight (11.02 KD), theoretical pI (4.20),Protein Isoelectric Point as pH 3.97and Aliphatic index as 78.57 and Grand average of hydropathicity (GRAVY): -0.405. PSORT Signal score as (-10.24), cytoplasmic protein score (0.650), mitochondrial matrix space (0.100), lysosome lumen score (0.100), Endoplasmic reticulum (0.00) and Possible cleavage site was (61).GOR- 4 predict secondary structure of HPV type 16 E7 protein in row as H=helix, S= extended ‘or’ Beta and C=coil and give the probable value for each amino acid. IMutant2.0 is used gives prediction of protein stability changes upon mutation. TCOFFEE was employed to compare the sequences which predict the key residues responsible for catalytic activity of the enzyme, amino acid sequence of HPV TYPE 16 E7 proteins.