This is a quite conservative approach, although it can still lead to errors. Following the automated assignment of function, we recommend that the user of WIT/WIT2 make a pass through the set of ORFs that have strong similarities to other proteins with known functional roles but for which no automated assignment could be made. WIT2 allows the user to peruse the BBHs for each protein, to align the protein against other proteins of known function, to analyze regions of similarity, and so forth. At this point, assignment of function is still a process of thoughtfully considering a wide range of alternatives, and the background of the user determines the quality of the assignments. We believe that the rapid addition of new genomes and the accumulation of a growing body of probable assignments of function, together with consistency checks based on clustering protein sequences, will lead to a situation in which most of the currently required judgment can be eliminated. However, we are not yet close to that point.