Performance of Iterative Methods. The individual 2,521 benchmarking sequences were used to iteratively search a non-redundant version of NCBI's NR database. The iterative models created from this process were then scored against the test database. The results of the searches were combined and scored. This procedure was then repeated for each of the 1000 bootstrapping replicate testsets. The average number of true positives was plotted versus errors per query. Minimum and maximums numbers of true positives from the replicates are shown as error bars. JackHMMER (Red) detects an average of 1,337 more homologs than SAM 3.5's target2k (Blue) and an average of 2,476 more homologs than NCBI's PSI-BLAST (Black) across the errors per query range. This represents an increase of 14% and 28% in remote protein homologs detected. As before, the total number of true homologous pairs between the 2,521 models and the test database is 39,733, and thus 12,000 true positives correspond to identifying 30% of the homologs.