A computer module that includes multiple alignments, secondary structure prediction, and site and pattern search has been developed and integrated into our ANTHEPROT software for protein sequence analysis. All the programs can be invoked from within any routine, thus yielding multiple pathways to obtain final results. All the results are graphically displayed. The main feature of this module is that all methods are connected in an interactive graphic manner. This module has been designed to display easily the potential sites with conserved predicted structures.