Figure 2

Tests to determine the optimum length criterion value. The fraction of candidate pairs that pass the triangle inequality test and the fraction that have the same number of domains increases with stricter (higher) length tolerance. In contrast, the number of predicted orthologous relationships decreases with stricter length tolerance. To consider only alignments that cover at least a fraction of the sequence length, a length criterion value of ℓ = 0.61 is used in this study.