Table 5

Fit parameters for the HMM

HMM n = 0

HMM n = 1

LQ

LS

λ

104 λ2

103K

λ

104 λ2

103K


348

150

0.2890 ± 0.85%

49.4722 ± 7.27%

0.2310 ± 9.32%

21.4600 ± 66.56%

200

0.2894 ± 2.84%

50.0796 ± 24.47%

0.2274 ± 1.74%

20.1017 ± 13.25%

300

0.2895 ± 2.69%

53.3472 ± 24.00%

0.2240 ± 4.86%

17.8934 ± 37.22%

348

0.2988 ± 3.24%

72.2356 ± 30.15%

0.2234 ± 2.39%

16.8704 ± 18.79%

360

0.2895 ± 1.79%

51.9056 ± 16.04%

0.2220 ± 2.14%

16.3757 ±16.52%

400

0.2859 ± 3.49%

48.4496 ± 31.10%

0.2232 ± 2.40%

17.5141 ± 18.94%

500

0.2912 ± 6.63%

54.0687 ± 61.22%

0.2182 ± 2.39%

14.7371 ± 19.10%

600

0.2901 ± 3.38%

51.9412 ± 31.74%

0.2180 ± 2.59%

14.2439 ± 20.86%


HMM n = 2

HMM n = 3

LQ

LS

λ

104 λ2

K

λ

104 λ2

K


348

150

0.1968 ± 0.70%

2.9247 ± 1.37%

12.0400 ± 6.48%

0.1767 ± 0.44%

2.6797 ± 1.01%

7.4435 ± 3.72%

200

0.1947 ± 2.12%

9.8704 ± 14.29%

0.1795 ± 0.46%

2.3586 ± 0.92%

8.5733 ± 3.87%

300

0.1937 ± 3.60%

9.9597 ± 25.32%

0.1863 ± 0.41%

2.0008 ± 0.94%

11.7859 ± 5.63%

348

0.1888 ± 3.19%

8.1338 ± 22.42%

0.1876 ± 0.32%

1.9328 ± 0.89%

12.1223 ± 3.83%

360

0.1926 ± 3.17%

9.7957 ± 22.82%

0.1853 ± 0.27%

1.9530 ± 0.65%

10.8640 ± 2.65%

400

0.1934 ± 1.05%

9.9321 ± 8.22%

0.1757 ± 1.64%

7.1756 ± 11.58%

500

0.1919 ± 1.61%

9.3630 ± 12.32%

0.1783 ± 0.98%

7.7945 ± 7.18%

600

0.1912 ± 1.70%

9.3303 ± 13.25%

0.1768 ± 1.01%

7.4165 ± 8.19%


HMM n = 4

HMM n = 5

LQ

LS

λ

104 λ2

103K

λ

104 λ2

103K


348

150

0.1732 ± 0.47%

2.2119 ± 1.14%

7.4991 ± 6.08%

0.1710 ± 0.38%

2.0698 ± 0.92%

8.1950 ± 3.70%

200

0.1686 ± 0.28%

2.1187 ± 0.72%

6.4162 ± 3.14%

0.1657 ± 0.39%

1.8231 ± 1.14%

6.9148 ± 3.82%

300

0.1682 ± 0.36%

1.9635 ± 0.79%

6.5436 ± 4.22%

0.1599 ± 0.37%

1.7836 ± 0.79%

5.4451 ± 3.85%

348

0.1685 ± 0.35%

1.9408 ± 0.74%

7.3851 ± 3.34%

0.1580 ± 0.28%

1.7930 ± 0.68%

5.3049 ± 2.61%

360

0.1678 ± 0.42%

1.9421 ± 0.92%

6.5775 ± 4.07%

0.1605 ± 0.23%

1.7481 ± 0.50%

5.7512 ± 2.89%

400

0.1662 ± 0.18%

1.9782 ± 0.40%

6.4164 ± 2.32%

0.1587 ± 0.28%

1.7828 ± 0.73%

5.4513 ± 2.57%

500

0.1693 ± 0.24%

1.9047 ± 0.51%

7.0735 ± 2.11%

0.1587 ± 0.16%

1.7957 ± 0.40%

5.4770 ± 2.31%

600

0.1693 ± 0.17%

1.8994 ± 0.39%

7.1112 ± 2.06%

0.1575 ± 0.29%

1.8330 ± 0.58%

5.2125 ± 2.68%


HMM n = 6

HMM n = 7

LQ

LS

λ

104 λ2

103K

104 λ2

103K


348

150

0.1663 ± 0.49%

2.1403 ± 1.04%

7.9392 ± 5.83%

0.1646 ± 0.30%

2.1396 ± 0.65%

8.7088 ± 4.21%

200

0.1614 ± 0.25%

1.7767 ± 0.65%

6.7568 ± 2.30%

0.1574 ± 0.41%

1.7687 ± 1.17%

6.5219 ± 3.81%

300

0.1551 ± 0.28%

1.5986 ± 0.80%

5.2551 ± 3.18%

0.1514 ± 0.26%

1.4638 ± 0.62%

5.0238 ± 4.34%

348

0.1531 ± 0.20%

1.5993 ± 0.55%

4.9132 ± 2.71%

0.1482 ± 0.33%

1.4755 ± 0.77%

4.4535 ± 4.13%

360

0.1536 ± 0.34%

1.6036 ± 1.02%

4.9160 ± 3.41%

0.1490 ± 0.39%

1.4479 ± 0.93%

4.6858 ± 3.28%

400

0.1537 ± 0.27%

1.5713 ± 0.62%

4.9524 ± 3.05%

0.1494 ± 0.24%

1.4328 ± 0.70%

4.6867 ± 2.08%

500

0.1519 ± 0.23%

1.6229 ± 0.67%

4.6812 ± 2.14%

0.1472 ± 0.29%

1.4706 ± 0.63%

4.2881 ± 2.50%

600

0.1489 ± 0.15%

1.7148 ± 0.33%

4.2283 ± 2.16%

0.1460 ± 0.18%

1.5193 ± 0.49%

4.2679 ± 1.74%


HMM n = 8

HMM n = 9

LQ

LS

λ

104 λ2

103K

λ

104 λ2

103K


348

150

0.1595 ± 0.47%

2.2162 ± 1.01%

7.5355 ± 4.01%

0.1603 ± 0.23%

2.1517 ± 0.48%

8.0273 ± 2.17%

200

0.1534 ± 0.55%

1.8019 ± 1.46%

5.9224 ± 5.25%

0.1508 ± 0.14%

1.7854 ± 0.28%

6.3535 ± 1.89%

300

0.1473 ± 0.47%

1.3916 ± 1.24%

4.8483 ± 4.01%

0.1413 ± 0.12%

1.4118 ± 0.35%

4.2141 ± 1.43%

348

0.1458 ± 0.32%

1.3409 ± 0.85%

4.6141 ± 3.69%

0.1398 ± 0.10%

1.3281 ± 0.33%

3.9661 ± 1.44%

360

0.1469 ± 0.34%

1.2868 ± 0.90%

4.9271 ± 2.73%

0.1400 ± 0.16%

1.2888 ± 0.43%

4.0126 ± 1.79%

400

0.1440 ± 0.34%

1.3591 ± 1.05%

4.0064 ± 3.48%

0.1382 ± 0.25%

1.2954 ± 0.67%

3.7257 ± 2.14%

500

0.1433 ± 0.29%

1.3382 ± 0.85%

3.9952 ± 2.70%

0.1352 ± 0.14%

1.3472 ± 0.42%

3.1780 ± 1.68%

600

0.1416 ± 0.33%

1.3760 ± 0.94%

3.7782 ± 3.14%

0.1359 ± 0.13%

1.3399 ± 0.38%

3.3536 ± 1.49%


HMM n = 10

HMM n = 11

LQ

LS

λ

104 λ2

103K

λ

104 λ2

103K


348

150

0.1552 ± 0.14%

2.2225 ± 0.30%

6.7936 ± 2.08%

0.1455 ± 0.14%

2.3813 ± 0.15%

4.9660 ± 3.82%

200

0.1459 ± 0.22%

1.8336 ± 0.37%

5.7585 ± 3.30%

0.1417 ± 0.17%

1.8428 ± 0.35%

5.1264 ± 2.07%

300

0.1370 ± 0.22%

1.4024 ± 0.56%

3.8087 ± 1.79%

0.1324 ± 0.27%

1.3842 ± 0.68%

3.2129 ± 2.79%

348

0.1353 ± 0.15%

1.2962 ± 0.38%

3.5507 ± 1.68%

0.1316 ± 0.22%

1.2518 ± 0.69%

3.1546 ± 1.94%

360

0.1343 ± 0.13%

1.2830 ± 0.36%

3.4674 ± 1.39%

0.1297 ± 0.25%

1.2737 ± 0.52%

2.9445 ± 2.81%

400

0.1334 ± 0.16%

1.2602 ± 0.38%

3.2164 ± 1.71%

0.1302 ± 0.20%

1.2160 ± 0.56%

2.9704 ± 1.59%

500

0.1307 ± 0.16%

1.3013 ± 0.46%

2.8331 ± 1.22%

0.1280 ± 0.30%

1.2426 ± 0.86%

2.7433 ± 2.73%

600

0.1305 ± 0.23%

1.3097 ± 0.56%

2.8239 ± 1.82%

0.1257 ± 0.22%

1.2908 ± 0.55%

2.4921 ± 1.79%


The table shows the fit parameters of the score distribution Prob(S = s| # of helices = n) for 1 ≤ n ≤ 11 for LQ = 348 and different subject lengths. For entries, where λ2 is left out, a suitable fit (with a small reduced χ2 value) to the modified Gumbel distribution Eq. (15) was not possible and only the Gumbel parameters of the high probability region are shown.

Wolfsheimer et al. BMC Bioinformatics 2011 12:47   doi:10.1186/1471-2105-12-47

Open Data