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In the optimization of the discrete model, the maximum overhang limitation is imposed based on geometrical parameters.
There are several parameters that can be explored, such as precess-angle, local dwell time, Z-offset, and maximum overhang of the polishing spot at the edge.
Offset and orientation of motifs are selected based on the maximum correlation, restricted to the minimum overlap of 6 bp and maximum overhang of 2 bp.
OK_OLAP(s x, s y, m i, d i, h i ) returns true if the sequences s x and s y have a minimum overlap of m, a minimum identity of d%, and a maximum overhang of h.
First-round CAP3 parameter settings for percent match, overlap length, maximum overhang percent, gap penalty, and base quality cutoff for clipping were -p 90 -o 50 -h 15 -g 2 -c 17, respectively.
Transcript assemblies (TA) are constructed using the TIGR Gene Indices Clustering TGICLL) pipeline (3) with a minimum sequence overlap identity between two sequences of 95%, a minimum overlap between sequences of 50 bp and a maximum overhang of non-overlapping sequences of 20 bp.
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The CAP3 -p option specifies overlap percent identity cutoff, while the -h option specifies the maximum alignment overhang percentage.
The CAP3 -p option specifies overlap per cent identity cut-off, while the -h option specifies the maximum alignment overhang percentage.
TaGI assemblies from Dana Farber Cancer Institute [ 8] required a minimum match of 40 base pairs with greater than 94% identity in the overlap region and a maximum unmatched overhang of 30 base pairs.
Edited sequences were condensed into contigs or singletons using TGICL [ 70] with the default parameters of 40 bp overlap, a minimum of 95% identity and a 30 bp maximum mismatched overhang.
Assembly criteria include a 50 bp minimum match, 95% minimum identity in the overlap region and 20 bp maximum unmatched overhangs.
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