Exact(3)
Tompa et al. allowed overlaps between the predicted sites and removed such sites from sFP if each site overlapped with a known site.
In this step, we only allowed overlaps or gaps of up to 10 nt within the fusion junction to accommodate small errors in alignment that occur at the edges of the alignment.
In accommodating small errors in alignment that occur at the edges of the alignment, we only allowed overlaps or gaps of up to 10 nt within the fusion junction.
Similar(57)
Make sure that your program of study satisfies all the rules, both for major and BME minor degree, especially the rules related to allowed overlap between major and minor.
The threshold value of allowed overlap for both methods was set at 35%.
By introducing a threshold parameter on the allowed overlap, one can define precisely the line between 'fuzzy' and 'overlapping'overlapping
The threshold for allowed overlap can significantly affect the output: the more overlap is allowed, the more nucleosomes can be placed.
In regard to the overlap displayed between modules, we set such parameters to the algorithm so that the allowed overlap was limited to 35%.
We used LTRharvest [ 39] with the minimum distance between two LTR sequences (option-mindistltr) set to 2000 base pairs and allowed overlapping hits (option-overlaps).
Our method requires users to specify three parameters, namely the threshold for allowed overlap between adjacent nucleosomes, the prior Δ on nucleosome sizes and its weight λ.
The 'Exact' evaluation assesses annotations, which matched regarding span and entity type, whereas 'Overlap+Type' allowed overlapping spans for annotations of the same type and 'Overlap' let annotations to have different types.
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