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). |
