Table 6 |
|||||
|
True Positive Summary |
|||||
|
Alignments |
Better (count) |
Worse (count) |
Better (avg. (stdev)) |
Worse (avg. (stdev)) |
|
|
|
|||||
|
High Similarity |
model trim vs. optimal |
10 |
0 |
0.018 (0.014) |
0 |
|
|
|||||
|
robust trim vs. optimal |
8 |
0 |
0.019 (0.014) |
0 |
|
|
|
|||||
|
frequency trim vs. optimal |
11 |
0 |
0.015 (0.013) |
0 |
|
|
|
|||||
|
local trim vs. optimal |
15 |
0 |
0.024 (0.016) |
0 |
|
|
|
|||||
|
local trim + model trim vs. local |
4 |
6 |
0.013 (0.010) |
-0.009 (0.003) |
|
|
|
|||||
|
model alignment vs. optimal |
8 |
3 |
0.024 (0.031) |
-0.008 (0.003) |
|
|
|
|||||
|
robust alignment vs. optimal |
3 |
12 |
0.024 (0.013) |
-0.170 (0.170) |
|
|
|
|||||
|
frequency alignment vs. optimal |
8 |
1 |
0.022 (0.030) |
-0.012 |
|
|
|
|||||
|
Medium Similarity |
model trim vs. optimal |
14 |
1 |
0.056 (0.058) |
-0.009 |
|
|
|||||
|
robust trim vs. optimal |
14 |
0 |
0.061 (0.056) |
0 |
|
|
|
|||||
|
frequency trim vs. optimal |
13 |
1 |
0.053 (0.057) |
-0.009 |
|
|
|
|||||
|
local trim vs. optimal |
14 |
3 |
0.098 (0.084) |
-0.012 (0.005) |
|
|
|
|||||
|
local trim + model trim vs. local |
9 |
8 |
0.061 (0.056) |
-0.015 (0.009) |
|
|
|
|||||
|
model alignment vs. optimal |
10 |
2 |
0.039 (0.043) |
-0.020 (0.018) |
|
|
|
|||||
|
robust alignment vs. optimal |
2 |
19 |
0.062 (0.000) |
-0.250 (0.140) |
|
|
|
|||||
|
frequency alignment vs. optimal |
8 |
2 |
0.045 (0.043) |
-0.020 (0.018) |
|
|
|
|||||
|
Low Similarity |
model trim vs. optimal |
12 |
1 |
0.054 (0.066) |
-0.024 |
|
|
|||||
|
robust trim vs. optimal |
17 |
0 |
0.051 (0.055) |
0 |
|
|
|
|||||
|
frequency trim vs. optimal |
12 |
1 |
0.055 (0.066) |
-0.024 |
|
|
|
|||||
|
local trim vs. optimal |
18 |
2 |
0.110 (0.100) |
-0.280 (0.380) |
|
|
|
|||||
|
local trim + model trim vs. local |
10 |
3 |
0.041 (0.065) |
-0.013 (0.005) |
|
|
|
|||||
|
model alignment vs. optimal |
7 |
2 |
0.021 (0.014) |
-0.034 (0.022) |
|
|
|
|||||
|
robust alignment vs. optimal |
2 |
16 |
0.150 (0.050) |
-0.240 (0.170) |
|
|
|
|||||
|
frequency alignment vs. optimal |
5 |
3 |
0.022 (0.016) |
-0.029 (0.018) |
|
|
|
|||||
|
Numbers shown are the number of sequence pairs, out of 22 in each similarity group, whose percentage of aligned edges that are correct with respect to the Dali alignment are improved or worsened by at least 0.005, along with the average and standard deviation of the magnitude of the difference. In the case of alignments limited to the local alignment boundaries, the Dali alignment is also limited to the local alignment boundaries. Alignments are as described in Table 5. |
|||||
|
Sierk et al. BMC Bioinformatics 2010 11:146 doi:10.1186/1471-2105-11-146 |
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