Table 1.   Methods of Predicting Gene Function When Homologs Have Multiple Functions Highest Hit The uncharacterized gene is assigned the function (or frequently, the annotated function) of the gene that is identified as the highest hit by a similarity search program (e.g., Tomb et al. 1997). Top Hits Identify top 10+ hits for the uncharacterized gene. Depending on the degree of consensus of the functions of the top hits, the query sequence is assigned a specific function, a general activity with unknown specificity, or no function (e.g., Blattner et al. 1997). Clusters of Orthologous Groups Genes are divided into groups of orthologs based on a cluster analysis of pairwise similarity scores between genes from different species. Uncharacterized genes are assigned the function of characterized orthologs (Tatusov et al. 1997). Phylogenomics Known functions are overlaid onto an evolutionary tree of all homologs. Functions of uncharacterized genes are predicted by their phylogenetic position relative to characterized genes (e.g., Eisen et al. 1995, 1997).