Figure 3
From: 3PD: Rapid design of optimal primers for chromosome conformation capture assays
Scoring Function. The scoring function used to compare primers and primer tuples. Each component of the scoring function is weighted and weights are refinable by the user. The components are (in order of appearance): difference in melting temperature(s) (T m ) to ideal melting temperature(s) (Tm, opt), difference in GC content(s) (GC) to ideal GC content(s) (GC opt ), difference in primer length(s) (length) to ideal length(s) ($length_{opt}$), difference in distance(s) to the restriction site(s) (dist RSS ) to ideal distance (distRSS, opt), difference in self alignments (SA) to optimal self alignment value (SA opt ), difference in self end alignments (SEA) to ideal self end alignment value (SEA opt ), and (only for primer pairs): difference in pair alignments of the candidat tuple and the set to which the candidate could be added (PA max (pair ∪ set)/PAmax) and difference in pair end alignments of the candidat tuple and the set to which the candidate could be added (PEA max (pair ∪ set)/PEA max ), respectively.