Table 1.
Top 5 optimal spaced seeds.
| seed | HI [0,1] | HI [0.5, 1] | HI [0.3, 0.7] | PH [0.7] | Markov |
|---|---|---|---|---|---|
| 111**1*11**1*1*111a | 0.300273 (1) | 0.598730 (1) | 0.0875373 (6) | 0.466982 (2) | 0.68499 (2482) |
| 111*1**1*1**11*111b | 0.300265 (2) | 0.598713 (2) | 0.0876001 (3) | 0.467122 (1) | 0.68869 (1425) |
| 11*1*1*11**1**1111 | 0.300064 (3) | 0.598314 (3) | 0.0874004 (12) | 0.466131 (3) | 0.68301 (3359) |
| 111**11*1**1*1*111 | 0.300031 (4) | 0.598247 (4) | 0.0873905 (13) | 0.466015 (4) | 0.68588 (2145) |
| 111*1**1*111*111c | 0.300031 (5) | 0.598204 (6) | 0.0876591 (1) | 0.465521 (13) | 0.70225 (52) |
| 1111*111*1111d | 0.2950 (22472) | 0.5882 (22829) | 0.0832 (19513) | 0.4421 (25033) | 0.7094 (1) |
| 1111*111**1*111e | 0.2988 (470) | 0.5957 (508) | 0.0866 (249) | 0.4596 (747) | 0.7089 (3) |
| 111**1*1**11**1*111f | 0.2999 (17) | 0.5980 (14) | 0.0870 (65) | 0.4656 (12) | 0.6802 (4907) |
| 11111111111g | 0.2590 (46252) | 0.5167 (46252) | 0.0538 (46252) | 0.3002 (46252) | 0.6066 (46133) |
Top 5 optimal spaced seeds with weight 11 which are identified by hit integration are listed. The 5 seeds are ordered by HI [0, 1]. Each value indicates the sensitivity of the seed at the same row which is determined by the sensitivity measure at the same column. The number in the parentheses indicates the rank of the seed for each measure. The descriptions of the labeled seeds are as below; a: the optimal seed of HI [0, 1] and HI [0.5, 1], b: the default seed of PatternHunter, c: the optimal seed of HI [0.3, 0.7], d: the optimal seed computed by mandala, e: the seed representing 5th-order non-coding markov model in [5], f: the seed representing 0th-order non-coding markov model in [5], g: the default seed of BLAST.