Figure 1

Minimum Error Rate Relative to Mean Search Time. 250 randomly chosen benchmarking models were used in HMMERHEAD Viterbi searches of NRDB90 and the test database utilizing a range of θ and η values. All other parameters were kept at their default value (θ = 6, δ = 2, μ = 7, and η = 20). Plotting minimum error rate versus mean search time for searches using these parameter values reveals a dramatic increase in minimum error rate, relative to a minor decrease in search time, for θ and η parameter values greater than 6 and 20, respectively. This further supports our choice of these parameter values for HMMERHEAD's default settings. The total number of true homologous pairs between those 250 models and the test benchmark was 3,617. The number of true positives identified at these parameter settings at 0 false positives is 938 or 26% of the possible true positives.