Due to the PCR conditions the maximum product size was limited to approximately 1.5 kb.
Default parameters were used, with a 200-kb maximum product size to reduce potential artifacts; 10 PETs were removed due to this threshold.
Primers (see Additional file 2 for sequences) were designed to span the predicted exons forming the fusion breakpoint and to generate a maximum product size of 300 bp, which was considered optimal for amplification, purification, and sequencing.
Exon specific oligonucleotide primers flanking known BRCA1 mutations were designed using Primer3 software [ 26] and limited to a maximum product size of 200 base pairs in order to successfully amplify sheared DNA extracted from paraffin embedded tissue (sequences listed in Additional file 1).
In this study, we are interested in extracting the biclique graph that has the maximum product of cluster size and the set of channels common among cluster members.
The minimum and maximum aberrant PCR product size was expected to be the sum of the minimum/maximum fragment size in the RLL and required flanking genomic region for primer development.
Primers were designed for KASP LGC Genomics SNPNP assays using BatchPrimer3 (allele-specific primers and allele-flanking primers; Tm: optimum, 57°; minimum, 55°; maximum, 60°; max difference, 2°; product size: minimum, 50 bp; optimum, 50 bp; maximum, 100 bp).
The parameters were set as following: the word size was 9, the discontiguous word was 1, the maximal allowed deviation of hit product size was 100, the maximum mismatches allowed, and the maximum indels allowed were 1, respectively.
Assay primers were developed using BatchPrimer3 with an optimal primer Tm of 57°C (minimum 55°C, maximum 60°C, maximum difference between primers of 5°C), optimal product size of 50 base pairs (minimum 50 base pairs, maximum 100 base pairs) and the default settings were used for the remaining parameters.
For air separation, novel experimental measurements, showing an optimum particle size for maximum product oxygen purity, are accurately described by the model.
Flanking primers for all 48 loci were designed using Primer3 version 2.0 (Rozen and Skaletsky, 2000) with default parameters except for: product size = 150 250 bp, maximum melting temperature (Tm) difference = 1°C, and maximum poly X = 3.
