Till the end of June 2005, there are totally around 1500 complete and ongoing genome sequencing projects (see the GOLD at http://www.genomesonline. org/) around the world. Near two hundred and fifty bacterial genomes have already been completely sequenced and other seven hundreds more are currently underway. The availability of the tremendous amount of whole genome sequences has no doubt opened up new avenues for genome-wide innovative genome design and efficient synthetic biology research. With such abundant resources, we do indeed need to develop tools for analyzing these sequences and mining the genomic treasures among these species. By analyzing the whole genomes for similarities/differences and structural features, it has become possible to identify new genetic targets and investigate their roles. Our group is interested in studying the architectural structures of the various genomes by many novel methods used to characterize genome structure in natural living cells and investigating their use in genome design and engineering. To aid this kind of comparative genome analysis, we have developed efficient gene identification and functional annotation pipeline and also constructed tools that can plot numerous measures for all positions in a long DNA sequence and do multiple whole genome comparisons. In this report, we would like to present a package of integrated comparative analysis platform (iCAP) for comparing various genomes from sequence level to pathway level and use locally sequenced bacterial species as examples to present some of the discovered features for genome design.