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The efficient development of effective vaccines and therapeutics is perhaps the most challenging of the myriad promises of post-genomic biology. Fortunately, as the list of sequenced bacterial pathogens grows, so does the opportunity to use whole genome sequence as a potentially powerful tool in vaccine development. According to Rino Rappuoli, vice president of vaccine research at Chiron, genomic approaches can be valuable alternatives to conventional, largely empirical approaches, especially in cases where strain variations in surface protein sequences and cross-reactivity with human proteins have proven to be stumbling blocks. Rappouli’s group published pioneering work last year in which unassembled genomic sequence from a virulent Group B Neisseria meningiditis strain was used to identify surface-expressed and exported proteins as novel, conserved vaccine targets (Science 287:1816-1820). Work using a similar approach to mine Streptococcus pneumoniae sequence data was published earlier this year (Infection and Immunity 69:1593-1598). Many other genome-based studies appear Sequence paves way for new vaccines