Supplementary material for Overbeek et al. (1999) Proc. Natl. Acad. Sci. USA 96(6), 2896-2901.

Algorithm 1:

A simple procedure for forming groups of genes using PCBBHs.

1. Let S = {G}, where G is a gene with known function from a single pathway.
2. For each gene in S, compute the coupling bidirectional best hit (BBH) scores to any potentially related genes. For each of these potentially coupled genes, if the coupling score is above a threshhold (say, 0.6), add the coupled gene and all genes from PCBBHs that were used to compute the score to S.
3. Repeat step 2 until no new genes get added to S.