If high-quality draft sequence is used, and it appears that there is too little sequence conservation among target strains, one might relax specifications for 100% conservation among strains for diagnostic signature prediction. Calculations indicate that it is often possible to generate signatures if one allows a base to be considered 'conserved' if it is present in only a fraction of the genomes (e.g. 75%) rather than the standard requirement for 100% conservation when finished sequence data are used. We have used this 'ratio-to-win' option to generate signature candidates for some highly divergent RNA viruses (for which we have finished sequence), although usually our preference is to include degenerate bases, especially when there are only a few bases with heterogeneity among strains in a given signature candidate. Using a ratio-to-win approach may be particularly important for the generation of protein signature candidates, since draft target data severely compromises the ability to detect conserved strings of amino acids.