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Exact(8)
Due to the calculation overhead caused by the overlap check, the runtime yielding full convergence increased from 18 h without overlap check to 44 h with overlap check.
Overlap check : an overlap check can be done optionally for each match M of F k exp by testing its compatibility with the other fragments F j exp j≠ k.
Even without the overlap check, full convergence is only obtained after 18 h of calculation time (case 4, Table 1).
The overlap check can reduce the number of final peak assignment possibilities, but will increase the runtime.
The results obtained show that even the assignment ensemble obtained without overlap check indeed allows the localization of almost any interaction site on EIN (see Supplementary Figs S2 S4).
The overlap check does not increase here the number of unique assignments (SAR-value=0), but it increases significantly the number of peaks having a SAR value below 10 Å.
Similar(52)
No overlap checking is done, since all obtained parallelograms detect repeated words, other than w, from different sequences.
In the case when no reference annotation is available, or if one wishes to mutually compare multiple annotations, BEACON processes each annotation as previously mentioned including overlap checking.
The putative contigs overlap were checked with Tablet (Milne et al. 2010), merging those contigs with no mismatches or gaps in the overlapping regions.
PCR primers were designed for sequence tag sites (STS) within the BAC-end sequences (SP6 and T7 ends) of suspected overlapping BACs spanning the hemoglobin gene region, and overlaps were checked by PCR amplification of the STS within the putative overlapping BACs.
Overlaps are checked against the FirstEF (First-Exon Finder), a 5′ -terminal exon and promoter prediction program.
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