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Nucleic Acids Res. (2009) 37, W647–W651

The authors wish it to be known that, following publication, they have discovered an error in the evaluation program of the original Web Server tool described in their article. The new approach still performs better and therefore the qualitative results and discussion remain valid. Table 1 in their article should however be replaced with Table 1 shown below and the last five sentences of the ‘Results’ section should read as follows:

Table 1.
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Comparison of the accuracy of breakpoint intervals (BPIs) predicted by jpHMM and the accuracy of BPI of fixed length

ThresholdBPI length
Percentage of BP found using
tBPIAverageMin/MaxPpostFixed BPI length
0.7516.120/11354.1759.44
0.8522.460/12168.0666.67
0.9026.892/13574.7269.72
0.9534.052/20281.1175.56
0.9948.585/23392.5082.78
0.999984.7711/49298.0692.50
ThresholdBPI length
Percentage of BP found using
tBPIAverageMin/MaxPpostFixed BPI length
0.7516.120/11354.1759.44
0.8522.460/12168.0666.67
0.9026.892/13574.7269.72
0.9534.052/20281.1175.56
0.9948.585/23392.5082.78
0.999984.7711/49298.0692.50

Results are shown for the first data set. In Column 1, the threshold tBPI is given. The average length of the BPI defined by tBPI is given in Column 2, the minimal and maximal length in Column 3. In Column 4, the percentage of real breakpoints detected with these BPIs is shown and in Column 5, the percentage of breakpoints using the average length of the predicted BPI as fixed BPI length (naïve method). For each threshold, the highest value is marked in bold face.

Table 1.
Open in new tab

Comparison of the accuracy of breakpoint intervals (BPIs) predicted by jpHMM and the accuracy of BPI of fixed length

ThresholdBPI length
Percentage of BP found using
tBPIAverageMin/MaxPpostFixed BPI length
0.7516.120/11354.1759.44
0.8522.460/12168.0666.67
0.9026.892/13574.7269.72
0.9534.052/20281.1175.56
0.9948.585/23392.5082.78
0.999984.7711/49298.0692.50
ThresholdBPI length
Percentage of BP found using
tBPIAverageMin/MaxPpostFixed BPI length
0.7516.120/11354.1759.44
0.8522.460/12168.0666.67
0.9026.892/13574.7269.72
0.9534.052/20281.1175.56
0.9948.585/23392.5082.78
0.999984.7711/49298.0692.50

Results are shown for the first data set. In Column 1, the threshold tBPI is given. The average length of the BPI defined by tBPI is given in Column 2, the minimal and maximal length in Column 3. In Column 4, the percentage of real breakpoints detected with these BPIs is shown and in Column 5, the percentage of breakpoints using the average length of the predicted BPI as fixed BPI length (naïve method). For each threshold, the highest value is marked in bold face.

For example, for the default threshold, only 82.78% of all breakpoints could be detected with the naïve method, compared with 92.50%. So, the sensitivity of our method is up to 9.72 percentage points higher than that of the naïve method. For the other two data sets, the results are similar.

For the sequences containing segments of length 500 nt, for the default threshold, only 69.97% of all breakpoints could be detected using breakpoint intervals of fixed length, compared with 82.72% with our method. For segments of length 300 nt, this is 80.5% compared with 87.5%.

© The Author(s) 2010. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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