Triplexator and Triplex Domain Finder

Triplexator and Triplex Domain Finder are computational frameworks⁴¹ for the in silico prediction of triplex structures. Triplex (nucleic acid triple helices) formation is governed by sequence-specific binding rules. The triplex-forming oligonucleotides (TFO) are located in the region of the single stranded nucleotide (RNA) capable of forming Hoogsteen (or reverse) bonds with the duplex⁴². The triplex target site (TTS) is defined as the polypurine-polypyrimidine tract of a duplex (DNA) capable of accommodating the TFO. An in silico triplex search was performed using Triplexator v1.3.2 with the PARTICLE RNA and selected regions of the human genome (UCSC assembly hg19; promoter and gene associated regions) as single stranded and double stranded inputs, respectively, employing parameters: a maximal error rate = 10, number of consecutive matches in a feature = 10, a minimum triplex length of 15 bp, a maximum triplex length of 30 bp, tolerated number of consecutive errors = 1. Triplexator software can be accessed using the virtual machine (http://bioinformatics.org.au/tools/triplexator/inspector/vm_guide.html). Assessment of the triplex target sites number/gene was determined followed by abundance sorting.

Triplex Domain Finder (TDF) was utilized for a more extensive search to determine whether PARTICLE could form triplexes extensively throughout the mouse (GRCm38.p4) and human (GRCh37/hg19) genomes. The parameters utilized were similar to those for Triplexator but also included the following: cut off value for RNA accessibility = 500.