True-positive and false-positive diagonal predictions in Arabidopsis chromosome 1 × 1 under various DiagHunter search parameters. Compare with false-positive predictions shown in Figure 5. True and false positives are judged relative to predictions reported in the literature [18, 19, 22, 23]. At low matrix compression factors, some diagonals are missed (bold graph lines), and those that are identified are fragmentary (thin solid graph line). At higher compression factors, random background hits should begin to 'merge' to give false-positive predictions. This has not occurred in these parameter ranges (dotted graph lines), though the program did mistakenly predict short diagonals in dense clusters of locally duplicated genes at low compression factors, particularly at less stringent diagonal quality thresholds (lines with asterisks). Parameters used in Figures 1 and 3 are: quality = 9, bit score = 650 (approximately corresponding in this dataset to BLAST expect values of < 10-68), compression factor = 26. These selections are indicated in a vertical line in the graph. Abbreviations: q, diagonal quality; sc, bit score; cf, compression factor.